{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/Emit3-HA-IP-Rep1.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/Emit3-HA-IP-Rep2.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/Emit3-CS-HA.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/Experimental_overview_and_rawfiles.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160627_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_sample2_2WT_C3_40per.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160509_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_CoIP_WT_25per.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160509_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_CoIP_MIP_25per.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20190930_QExHFX1_RSLC1_Tian_Loidl_MFPL_C2S_2509_40p.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20190930_QExHFX1_RSLC1_Tian_Loidl_MFPL_WT_2509_40p.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160627_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_sample1_2MIP1_C3_25per.raw"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160509_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_CoIP_WT_25per.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160627_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_sample2_2WT_C3_40per.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20190930_QExHFX1_RSLC1_Tian_Loidl_MFPL_C2S_2509_40p.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160509_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_CoIP_MIP_25per.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20190930_QExHFX1_RSLC1_Tian_Loidl_MFPL_WT_2509_40p.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/20160627_QexHF4_RSLC4_Tian_Loidl_MFPL_coom_sample1_2MIP1_C3_25per.mgf"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD057568/Tt_ciliateorg14_broad_nr.fa"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["miao.tian@ouc.edu.cn"],"submitter":["Miao TIAN"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry"],"software":[""],"submitter_keywords":["Immunoprecipitation","Tetrahymena thermophila","Lc-ms/ms","Meiosis","Ncrna transcription"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD057568"],"tissue":["Cell Culture"],"sample_protocol":["Immunoprecipitation (IP) was performed similar to the protocol in (Tian et al. 2017). Briefly, IP from conjugation cells was performed with both partners expressing C-terminal HA tagged proteins (Emit3, Emit3-CS). Cells were grown to OD540nm ≈ 0.7 in 200 ml of growth medium, washed with 10 mM Tris-HCl (pH 7.5), and starved in the same buffer. 3 ~ 3.5 hours after mixing, the paring rate and the progression of conjugation were examined. IP was performed only if over 80% of cells were conjugated and their MICs were elongating. Conjugation cells were lysed in a Dounce Homogenizer with 10ml lysis buffer (30mM Tris-Base, 20mM KCl, 2mM MgCl2, pH8.1, 150mM NaCl, 0.1% Triton X-100, 1mM PMSF, cOmplete EDTA-free protease inhibitor). Lysed cells were then spin for 50 min at 4 degrees at 25,000 rpm in an ultra-centrifuge. After that, supernatants were filtered with a PVDF 0.45um filter. In order to enrich HA-tagged proteins, 200μl of EZview Red Anti-HA Affinity Gel (Sigma) were used for each sample. Beads were first equilibrated in wash buffer (30mM Tris-Base, 20mM KCl, 2mM MgCl2, pH8.1, 150mM NaCl, 0.1% Triton X-100, cOmplete protease inhibitor) and then mixed with the precleared cell lysate, then incubated for 2 hr at 4 degrees with slow rotating. After that, beads were washed 3 times with 1 ml wash buffer and once with T0 buffer (30mM Tris-Base, 20mM KCl, 2mM MgCl2, pH8.1, 1mM PMSF, cOmplete protease inhibitor). After the last wash, 400μl of HA peptide (250μg/ml in wash buffer) was added to the beads and incubate at 25 degrees for 20min to elute HA-tagged proteins and their associated proteins. After elution, proteins in eluents were precipitated with TCA and then loaded into a 12% SDS-PAGE gel. After the loading dye run into the gel for ~ 3 cm, gel electrophoresis was stopped, and the gel was stained with Coomassie brilliant blue R250 dye. After destaining, gel pieces with stained proteins were cut and soaked in ultra-pure water for the downstream in-gel tryptic digestion. Gel bands were excised and after reduction and alkylation of thiols using dithiothreitol and iodoacetamide the proteins were digested with trypsin as described by Shevchenko et al.(2007) with slight modifications. After digestion the peptide solutions were desalted on custom-made C18 stagetips (Rappsilber et al., (2007)). Tryptic digests were separated on an Ultimate 3000 RSLC nano-flow chromatography system (Thermo Fisher Scientific), using a pre-column for sample loading (PepMapAcclaim C18, 2 cm × 0.1 mm, 5 μm) and a C18 analytical column (PepMapAcclaim C18, 50 cm × 0.75 mm, 2 μm, Dionex-Thermo-Fisher Scientific), applying a linear gradient from 2 to 35% solvent B (80% acetonitrile, 0.1% formic acid; solvent A 0.1% formic acid) at a flow rate of 230 nl min−1 over 120 minutes. Eluting peptides were analysed on a Q Exactive HF Orbitrap mass spectrometer, equipped with a Proxeon nanospray source (all Thermo Fisher Scientific). For the data-dependent mode survey scans were obtained in a mass range of 380–1,650 m/z with lock mass on, at a resolution of 120.000 at 200 m/z and an AGC target value of 3E6. The 10 most intense ions were selected with an isolation width of 2.0 Da, fragmented in the HCD cell at 27% collision energy and the spectra recorded at a target value of 1E5 and a resolution of 30000. Peptides with a charge of +1 or > +6 were excluded from fragmentation, the peptide match and exclude isotope features were enabled and selected precursors were dynamically excluded from repeated sampling for 30 s."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw data were processed with MaxQuant software package 1.5.2.8/1.5.5.1 (http://www.maxquant.org/) (ref: Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008)) searching against a tetrahymena database (www.ciliate.org, version 2014 supplmented with sequences from www.jcvi.org build 2014; the FASTA files used are uploaded with the raw data) and a custom contamination database, with tryptic specificity allowing two missed cleavages. Carbamidomethylation was set as fixed modification, oxidation of methionine, N-terminal protein acetylation, phosphorylation of serine, threonine and tyrosine as variable modifications — all other parameters were set to default. Results were filtered at a protein and peptide false discovery rate of 1%."],"omics_type":["Proteomics"],"labhead":["Miao TIAN"],"instrument_platform":[""],"labhead_affiliation":["MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China"],"submission_type":["PARTIAL"],"species":["Tetrahymena Thermophila"],"submitter_mail":["miao.tian@ouc.edu.cn"],"publication":["10.1093/NAR/GKAF427"],"submitter_affiliation":["Ocean University of China"],"submitter_country":["China"],"description_synonyms":["Non Protein Coding, Ribonucleic, Transcription Factor IIB, RNA pol II, DNA Insertion, DNA Transposable Element, sci, RpII215, RpII140[wimp], synaptic ribbon, Noncoding RNA, protein polypeptide chains, Mediator Like Complex, RNApol2, Insertion Sequence Elements, HOW, How, Thyroid Hormone Associated Protein Complex, 5, dmTFIIB, Sequence Element, Non Polyadenylated, Theory, Utility Theories, RNApolII, Mediator-Like Complex, Tes1, Non-Protein-Coding RNA, Mediator Transcription Complex, Mediator Like Complexes, Economic Policies, stru, proteins, Tes2, Living Costs, l(3)S053606, pre-synaptic ribbon, Srb-mediator complex, TF2B, epiphyseal dysplasia, Non Coding, DNA Dependent RNA Polymerase II, Insertion Sequence, Role Concepts, Household Consumptions, Economic, CG1554, stage, Precipitations, transcription from bacterial-type RNA polymerase promoter, Pol II0[ser2], LC-MS2, Zn(II), EIEE13, RNA Pol II 140, T-bar ribbon, Indices, Index, PolII, zincum, Economic Condition, DNA Insertion Element, tess, Role Concept, Zn2+, ribbon, Playthings and Play, Non-Coding RNA, Utility Theory, Dm6, Role, Ribonucleic acids, Macroeconomic, cinc, TESS, DmelCG3180, Acid, Pol-IIa, RPB6_DROME, ARABIDOPSIS NPK1-ACTIVATING KINESIN 2, Consumer Price Indices, PolIIo, RNAP II LS, Non-Protein-Coding, TETRASPORE, Home, Genomic, Pol II0[ser5], DNA Transposons, Condition, multiple, liquid chromatography-tandem mass spectroscopy, H5, DNA, dRPB1, dRpb1, DmelCG3284, dRPB9, Transposable Element, Policies, Nontranslated RNA, npcRNA, developmental stage, Utility, CG1163, Genomic Stability, protein-containing complex, presynaptic ribbon, zinc, Easterlin, II, Pol II, IS, LC-MSMS, Genomic Instabilities, dTES, Gene Products, Immune Precipitations, Genome Instabilities, Immune Precipitation, Toy, DmelCG6522, l(3)RplII140, Sequence Elements, medea, Playthings, Non-Coding, Pol II CTD, Rpll18, Microeconomic Factors, RNAPII0, E(zen)3, RNANC, Tn Elements, Transposons, Zink, Puppets, L5, Capital, TRAP (Thyroid Hormone Associated Protein) Complex, l(1)DF912, Pol IIo[ser5], Puppet, Drl, DNA Insertion Elements, Pol IIo, RNA, Conditions, Pol IIc, Pol IIa, Proteins, TR-Associated Protein (TRAP) Complex, RNS, Factor, qkr, l(3)S090417, RNAPII, Mdu, DmelCG1163, Concept, Insertion Sequence Element, RPB2_DROME, native protein, Consumer Price Index, Consumer Price, CG3284, mda, T-bar., MED, KH93F, CDK8-containing TRAP/mediator complex, chemical analysis, bHLHa13, Transposable Elements, ami, Transposon, underdeveloped, med, Pol IIo[ser2], Ribonucleic Acid, N-tris(hydroxymethyl)methyl-2-aminomethane sulfonate, l(1)10Ca, Gene Proteins, Pol II[ser2], Genome Instability, NaCh6, NPK1-ACTIVATING KINESIN 2, RNA Polymerase B, CTD, liquid chromatography tandem mass spectrometry, Noncoding, CG6522, DNA-Dependent RNA Polymerase II, RNA PolI 215, PN4, Instability, l(3)XIIm137, liquid chromatography tandem mass spectroscopy, Co-Immunoprecipitations, Insertion, determination, Transposable, l(3)Z23, 8WG16, Pol-II, protein, Genome Stability, pre-synaptic dense body, CG11121, dTfIIB, Co Immunoprecipitation, old, RNA polII, l(1)L5, active zone cytomatrix, Roles, POL, RNA pol IIo, PHPVAR, Concepts, Pol IIo[Ser2], protein aggregate, Microeconomic, l(3)j5D5, RNA Gene Products, TfllB, 24B, tess-2, EDM1, EDM2, EDM3, LCMSMS, Household Consumption, Elements, Rpll140, Co-Immunoprecipitation, hypoplasia, Precipitation, CG10293, SO, NACK2, l(3)j5B5, Immune, 30Zn, Math5, anon-EST:Posey121, CG3180, polII, Theories, EPD1, So, l(3)12m-137, IS Element, 0904/17, Home Economics, DJ39G22.4, IDD, ribose nucleic acid, Hypothesis, ribonucleic acids, LC-MS/MS, Tn Element, l(1)DC912, Tn, Macroeconomic Factors, Economics, Household, SZ1, Tetrahymenas, Ribonukleinsaeure, l(3)88Be, Plaything, pentosenucleic acids, Mediator-Like Complexes, Non-Peptide-Coding, dSmad4, TESS-2, CERIII, pol II, DmelCG1554, Element, Insertion Elements, Factors, Rpb2, RNA Pol II, Rpb1, RPB1, Toys, Nontranslated, RpABC14, TRAP complex, Pol II Ser5P, Easterlin Hypothesis, dTFIIB, testin2, bacterial transcription, RPII18, anon-EST:Liang-2.39, RPII15, Genomic Stabilities, Remittances, rpII140/wimp, CIAT, Plays, DJ885L7.4.1, DmelCG1775, PSACH, P62, Gene, Insertion Element, LC-MS-MS, Stability, PolIIc, pre-synaptic cytoskeletal matrix assembled at active zones, reduced, polypeptide chain, DmelCG11121, Instabilities, l(3)SG36, Thyroid Hormone-Associated Protein Complex, tiny, life cycle stage, somda, l(3)s2612, CG5193, RNAP, RPII215, Zn, BcDNA:RH21608, Economic Conditions, Ubl, Non-Polyadenylated RNA, SMAD4, RNAP II, DmelCG10293, L mediator complex, Nav1.6, Play, RNA Pol II CTD, Smad4, l(1)G0040, DNA Transposon, small, Policy, RNA PolII, Economic Policy, Non Peptide Coding, clone 2.39, protein complex, l(3)11m-254, Production, Living Cost, Consumption, Stabilities, IS Elements, Non-Peptide-Coding RNA, LC/MS/MS, RPII140, developmental_stage, natural protein, yeast nucleic acid, STL5, Protein, RNA Pol IIc, TFIIB, DmRP140, Rpll215, Untranslated RNA, Genome Stabilities, development stage, CG1775, CAZ, who, Tfiib, ribonucleic acid, wimp, RP140, presynaptic cytomatrix assembled at active zones, Non Polyadenylated RNA, ATNACK2, THBS5, Non-Polyadenylated, INSDC_qualifier:other, Who/How, RpII, l(3)SG70, DmelCG5193, NCRNA, DNA Transposable, Protein Gene Products, Remittance, Cost of Living, presynaptic dense body, D6Ertd352e, qkr[93F], assay, Genome"],"sample_synonyms":["Water, sodium salt, Dyes, CPD photolyase activity, Dinitrilotetraacetate, ammonium formate, Ethylenedinitrilotetraacetic Acid, 13C-labeled, MeCN, cadmium salt, odd(Oz), muriate of potash, PhrB photolyase activity, ion, Compounds, Potassium EDTA, Design, H(2)O, Octoxinols, Triton X305, BOUND WATER, magnesium formate, Survey Methods, oxidane, zinc salt, Questionnaire Designs, heavy chain disease, Solvent, WATER, Dicobalt, l(2)k09905, HOH, l(1)AA33, Thiol, dmTAF[[II]]230, Polypeptides, hydrogen chloride, Edetic, Magnesium chloride, MSK16, cobalt(II) formate dihydrate, Protease Inhibitor, dyes, Survey Methodology, CH3-C#N, ten-m, B1, 1, DGS, 2, 3, NUP96, sylvite, epithelium, Randomized Response, WMS, (R*, Octoxynol-9, Disodium Salt, DmelCG8428, Spin, Divorced, Polyacrylamide, l(3)rP126, SDS-PAGE electrophoresis, TFIID TAF250, cel, Glycine, DmelCG13176, N, Tissue, Basen, ORF19, proteins, Divorces, BcDNA:AT25108, Edetate, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, salt, SPIN, Wasserstoffchlorid, Peptidohydrolase Inhibitor, column, l(1)B2/13.1, BTKAP1, sample, D1, 2-Ethanediylbis(N-(carboxymethyl)glycine), RED, Red, CT, autolysin activity, Precipitations, Gallium EDTA, GTFII-I, Octylphenoxy Polyethoxyethanol, Inorganic, nickel salt, SGS, Ten-mc, 6030441I21Rik, Thiols, dTAF[[II]]230, Klor-con, l(1)LB9, Mercaptans, cobalt (+2) salt, Dipotassium Salt, Mercapto Compounds, CG5723, Ct, TAF200, Pigments, BAP135, Questionnaire Design, Triton X100, HMG-CoAR, CSA2, ACMICD, MgCl2, H2O, common salt, sodium (4:1:1) salt, Dm1, magnesium salt, Organic Pigments, Base2, Base1, Hydrolase Inhibitor, Chlorwasserstoff, Magnesium Salt, dipyrimidine photolyase (photosensitive), BAP-135, 1110049F14Rik, Chromium EDTA, Hydrogen Oxide, Acid, Antagonists, Sodium Dodecyl Sulfate-PAGE, Nonrespondent, formate, cromium (+3), N'-1, GtfII-I, study protocol, beta Trypsin, Agc, CG1106, Sodium Salt, l(2)W5, Taf250, xylene brilliant cyanine G, Charges and Fees, bacteriolytic toxin activity, ammonium (4:1) salt, Surveys, 2017, Monopotassium chloride, 3-tetramethylbutyl)phenyl)-omega-hydroxy-, Edetate Disodium Calcium, Endopeptidase, Peptide Peptidohydrolase Inhibitor, methyl cyanide, chlorane, Sodium Dodecyl Sulfate-PAGEs, Disodium Versenate, lead (+2) salt, 4-Dimercapto-2, Polyethoxyethanol, TAF230, Community, Ethylenediaminetetraacetic Acid, Cleland Reagent, Gallium, N5-carboxyaminoimidazole ribonucleotide mutase activity, rac-Dithiothreitol, 5301, l(1)VE614, nickel formate dihydrate, lead formate, chlorure d'hydrogene, Endopeptidase Inhibitors, threo-1, Cleland's reagent, Sulfhydryl, aluminum salt, Ethylenediaminetetraacetic, 4-dimercapto-, Gel Electrophoresis, R*)-, SDS polyacrylamide gel electrophoresis of proteins, thomson, 2-ethanediyl), body system, CG7826, deoxyribodipyrimidine photolyase activity, agua, C.I. 42655, mass-to-charge ratio, Agent, Odz, Electrophoreses, Magnesium Disodium, Triton X 305, PVDF, Polyacrylamide Gel Electrophoresis, Community Survey, Immune Precipitations, Gene Products, CG7835, Baseline Surveys, CG42273, system, Randomized, PMSF, Randomized Response Techniques, Peptide Hydrolase, Coloring Agent, Immune Precipitation, odz, anatomical systems, FAM39E, dTAF[[II]]250, Hydrogen chloride, thallium (+1) salt, cell, Monosodium Salt, homopolymer, beta-Trypsin, rubidium salt, F23A5.3, Farbstoff, Respondent, methanoic acid, Questionnaires and Surveys, ions, l(3)rJ307, alpha-(4-(1, Antagonist, supranol cyanine G, kf, Solution, l(3)05301, Tetracemate, dTAF250, Triton X45, Protease Antagonists, Stannous EDTA, Kochsalz, Peptide Peptidohydrolase Inhibitors, serva blue G, peptidos, Immobilon CD, Chromatographies, Potassium, PTHB1, CSPG1, SDS PAGE, LB5, 3-butanediol, WBSCR6, Magnesiumchlorid, An4, 1-(14)C-labeled, Proteins, Octoxinol, Stannous, Clelands Reagent, Coprin, chloridohydrogen, potassium formate, BG:DS00004.13, copper (+2) salt, Immobilon P, Rnt, acetonitrile, buffer, Copper, Cell, Dithiothreitol, 1-difluoro-, Ten79E, bnch, dTAF230, Kaliumchlorid, Versene, lLB5, l(2)k02511, polypeptide, Triton X 100, Wash2, Mercaptan, Wash1, Organic, N5-CAIR mutase activity, native protein, Natriumchlorid, C18, cupric formate, TAF[[II]]250/230, MFS1, NaCl, Edathamil, aluminum formate, Magnesium chloride anhydrous, DTL, Cleland's, AU020952, Taf[[II]]250, Calcium, DTT, RPE, lithium formate, CT16449, holin, Sulfhydryl Compound, Response Technique, Ethylene Dinitrilotetraacetate, sodium dodecyl sulphate–polyacrylamide gel electrophoresis, Separations, Chloride, Monopotassium Salt, ethanenitrile, Peptidohydrolase Inhibitors, REDK, Stains, Magnesium Disodium EDTA, ME-IV, p. pigmentosa retinae, plan specification, xnup93, Cleland's Reagent, Gene Proteins, Peptidase, Magnesium chloride (MgCl2), Antiprotease, Compound, Mercapto, Disodium Ethylene Dinitrilotetraacetate, Fees, ten(m), deoxyribonucleate pyrimidine dimer lyase (photosensitive), nucleobases, Peptide Hydrolase Inhibitors, [OH2], hydrochloric acid, Calcium Salt, Farbstoffe, CG11452, DIWS, Co-Immunoprecipitations, Triton X-45, Coomassie brilliant blue G 250, Endopeptidase Inhibitor, NCMe, Feature, leg, Triton X-305, classic hairy cell leukaemia, Peptide Hydrolase Inhibitor, zinc formate, KCl, lead salt, Ethylenedinitrilotetraacetic, protein, Hydrogenchlorid, pigmented epithelium, Calcium Disodium, Poly(oxy-1, alpha-toluenesulphonyl fluoride, Co Immunoprecipitation, Alkylations, polyvinylidene difluoride, peptide, Cut, DmelCG5723, Techniques, halite, ammonium tetraformate, peptido, Edetic Acid, Klotrix, l(1)7Ba, polyvinyldifluoride, l(1)7Bb, SDS-PAGE, Octoxynol 9, Inhibitors, Williams-Beuren syndrome chromosomal region 6 protein, Min, Nonrespondents, Hydrolase Inhibitors, Calcium Tetacine, DmelCG42273, class I PurE, Edetates, peptides, l(3)rL201, Co-Immunoprecipitation, ethene, bases, Dye, Precipitation, pigmented retina, Designs, min, ten-m/odz, mAPC, Questionnaires, Coomassie brilliant blue G250, copper, ten[m], CG11387, DNA cyclobutane dipyrimidine photolyase activity, Calcitetracemate, cloruro sodico, Calcium Disodium Versenate, Immune, lithium salt, Disodium Calcitetracemate, Respondents, Sputolysin, RUN, Run, DmelCG1106, Diws1t, dye, dihydridooxygen, brilliant blue G, Tetacine, necrosis, dihydrogen oxide, GPHYSD2, ammonium (2:1) salt, [KCl], PRE, Questionnaire, rock salt, teinture, Calcium Disodium Edetate, Peptidase Inhibitor, Nucleobase, [MgCl2], deoxyribonucleic cyclobutane dipyrimidine photolyase activity, aqua, Dmel_CG7826, Th, 4-dimercapto-2, classic hairy cell leukemia, TAFII-250, l(3)05309, Peptide Peptidohydrolase, TAF250/230, AA33, Triton X-100, Versenate, TAFII250, HCD, Cleland, retinal pigment, Ionen, Distannous EDTA, SRF-Phox1-interacting protein, bacteriocin activity, Kaon-Cl 10, WASH, BcDNA:GH10590, nickel (+2) salt, Copper EDTA, retinal pigment layer, Dmel_CG7835, Mnb, MNB, l(2R)W5, poly(vinylidene fluoride), ammonium salt, Distannous, HCl, hydrogen hydroxide, cobaltous formate, SDS polyacrylamide gel electrophoresis, 3-Butanediol, MASS, AW124434, natrii chloridum, Survey Method, CG17603, Features, TAF[[II]], PurE, acqua, organ system, R*)-1, nanospray, phr A photolyase activity, lysin activity, Peptidase Inhibitors, DNA-photoreactivating enzyme, Charge, WBS, AGC1, Acetamide, SR3-5, Base, copper salt, Antiproteases, CG8428, coomassie blue G, acid blue 90, Polypeptide, Wasser, 2-ethanediylbis(N-(carboxymethyl))-, Inhibitor, base, CG1849, d230, Organic Pigment, Reagent, cesium salt, FBN, Gene, Protease, dTAFII250, Ten[m], photoreactivating enzyme activity, EfW1, TFII-I, Buffer, Bruton tyrosine kinase-associated protein 135, formic acid, Potassium Salt, method, Sodium Dodecyl Sulfate PAGE, potassium salt, Octoxynols, Octylphenoxy, dmTAF1, ECTOL1, Taf230, p63, 14C-labeled, Baseline, method used in an experiment, p65, Pigment, IB291, Survey, Protease Antagonist, stratum pigmentosa retinae, AA673430, Separated, cloruro de hidrogeno, TAF250, Inorganic Pigments, hYAK3-2, Methodology, Taf200, MOS3, Ethylene, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PRECOCIOUS, iones, Runt, gel, chlorure de sodium, Taf1p, eau, colorante, calcium formate, Charges, OCTD, Benzenemethanesulfonyl fluoride, lysate, Chromium Salt, Fee, Octylphenoxypolyethoxyethanols, DmelCG11387, odz/ten-m, EDTA, 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase activity, Randomized Response Technique, cromium (+3) salt, AA553322, BTK-associated protein 135, Characteristics, TAF, Dicobalt EDTA, Disodium EDTA, teintures, 2-iodo-, F23A5_3, sodium formate, sampling., DYRK5, Repeated Rounds of Survey, DYRK1, data, TAF[[II]]250, nickel formate, 3H-labeled, DmelCG1849, strontium formate, l(3)84Ab, strontium salt, Magnesium, Peptide, alpha-toluenesulfonyl fluoride, Dithiotreitol, [HCl], Isotope, MODIFIER OF SNC1, Characteristic, colorantes, p230, water, Protein, DL-threo-1, deoxyribonucleic photolyase activity, Hydrochloride, TFIID, table salt, 25/11, Dyrk1, connected anatomical system, Disodium Ethylene, ACETONITRILE, cyanomethane, WMS2, CG13176, Methods, Tissue Stain, Community Surveys, Response Techniques, Separation, Tissue Stains, PRSS, TAF[[II]]230, phenylmethylsulfonyl fluoride, Chelaton 3, photolyase activity, Triton X 45, Dihydrate, CC1, Tripcellim, l(1)19Ea, TAF[II]250, Disodium, sample population, chromic formate, Protein Gene Products, l(2)10403, Coloring, P235, Stain, Trypure, Baseline Survey, sample collection, DmelCG17603, Ion, SSKS, calcium salt, Peptid, Chromium, l(3)00844, TAF1"],"name_synonyms":["liquid chromatography tandem mass spectroscopy, LC-MS2, Zn(II), Co-Immunoprecipitations, T-bar ribbon, determination, protein complex, Transcription Factor IIB, Proteins, LC-MS/MS, Gene, zincum, protein, protein-containing complex, presynaptic ribbon, pre-synaptic dense body, zinc, synaptic ribbon, LC-MS-MS, dTfIIB, Co Immunoprecipitation, protein polypeptide chains, LC/MS/MS, Zn2+, pre-synaptic cytoskeletal matrix assembled at active zones, native protein, ribbon, natural protein, polypeptide chain, active zone cytomatrix, T-bar., Tetrahymenas, LC-MSMS, chemical analysis, Protein, Immune Precipitations, TFIIB, Gene Products, cinc, dmTFIIB, protein aggregate, Immune Precipitation, CAZ, Tfiib, TfllB, LCMSMS, presynaptic cytomatrix assembled at active zones, CG5193, Co-Immunoprecipitation, Precipitation, Zn, proteins, DmelCG5193, pre-synaptic ribbon, Protein Gene Products, Gene Proteins, TF2B, Immune, 30Zn, Zink, dTFIIB, liquid chromatography-tandem mass spectroscopy, presynaptic dense body, liquid chromatography tandem mass spectrometry, assay, Precipitations"],"data_synonyms":["Bru, IPP2A2, para Tyrosine, cox4, 11alpha, Raw, TalANAc, 1.5.5.1, L-Threonine, protein, Electron-transferring-flavoprotein dehydrogenase, phosphorylation, 2-Amino-3-hydroxypropionic acid, 5730420M11Rik, peptide, Polypeptides, ref2p, protein polypeptide chains, L-Isomer Methionine, Methionine, peptido, Software Engineering, DmelCG10664, Gpi-1, protein aggregate, Computer Program, WMS, Threonin, ALY|REF, Svc, SET, peptides, ETF-QO, TAF-I, Nlk, COXIV, M, Open, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Computer Programs and Programming, proteins, Y, COXA_DROME, DmelCG4299, BEF, 13E, IGAAD, set, Cox4, 2-amino-3-hydroxypropanoic acid, DmelCG10574, Tyr, REF, 1.3.3.3, GPHYSD2, COX-VA, Racemethionine, SGS, NK/GPI, Gpi, phapii, DmelCG10360, 2-Amino-4-(methylthio)butyric acid, 2-Amino-3-(p-hydroxyphenyl)propionic acid, ref, StF-IT-1, para-Tyrosine, 2-(acetylamino)-2-deoxy-, Source Softwares, Software Tools, Fsrg1, Programs, ACMICD, Tyrosine, Program, Computer Applications, Ref2P, ref(2)Po2, RING3, mOC-X, 3-Hydroxyalanine, VA, Tetrahymenas, AL024441, Computer Applications Software, FSRG1, Computer Applications Softwares, Methionin, NK|GPI, Softwares, Hmet, COX IV, Org, ORG, Software Applications, HLA-DR-associated protein II, DI-2, Va, Coprogen oxidase, Source Software, I-2Dm, COX IV-1, L-isomer, Gpi1-r, Gpi1-s, MASS, CG4299, 15S)-, Gpi1-t, L isomer, I-2PP1, Applications, TAF-IBETA, Specificity and Sensitivity, (5Z, L Serine, TAF-Ibeta, L-Tyrosine, DmelCG14724, Polypeptide, L-Serine, i2pp2a, Liquimeth, Proteomes, Fsrg-1, Bglap-rs1, Cox4a, Gpi1s, Computer Software Applications, NAT, Nat, D17H6S113E, alpha-L-Talopyranuronic acid, 2-amino-4-(methylsulfanyl)butanoic acid, AI461847, Ref(2)P, L Isomer, FBN, Gene, alpha-L-N-acetyltalosaminuronic acid, Computer, protein-containing complex, FSH, PHAPII, CG10664, polypeptide chain, ECTOL1, Ref(2)p, p62, THOC4, IV, Gene Products, L-Methionine, Pgi, Del(8)44H, Pedameth, Application, Open Source Softwares, Coproporphyrinogenase, Gpi-1r, Software Application, Gpi-1s, protein amino acid acetylation, Phi, ALY/REF, ipp2a2, Gpi-1t, Open Source Software, 2pp2a, Ring3, L Threonine, CG10574, Computer Software Application, OCTD, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, L Tyrosine, taf-ibeta, COX, dSET, dSet, Sensitivity, peptidos, Tyrosin, metionina, ref(2)Pn, Applications Software, Open Source, data, Computer Software, DL-Methionine, protein complex, ALY, Proteins, igaad, Phosphorylations, total expressed protein, ref(2)p, ETF dehydrogenase, MF, L-Isomer, Amf, Peptide, Tool, group, polypeptide, Serin, Software Tool, native protein, natural protein, I-2PP2A, tirosina, AW228947, Protein, Dm I-2, I2PP2A, IV-1, MFS1, phosphorylation enrichment, mKIAA4005, Software, NK, WMS2, Data Base, Met, D6S113E, Col4a-1, ensemble, RNF3, Rnf3, Frg-1, Engineering, tend, Specificity, ETF-ubiquinone oxidoreductase, Protein Gene Products, Computer Programs, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, CG14724, Applications Softwares, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, CG10360, AA407739, Peptide., alpha-L-2-N-acetylamino-2-desoxytaluronic acid"],"additional_accession":[]},"is_claimable":false,"name":"LC-MS/MS analysis of immunoprecipitation samples of a Tetrahymena TFIIB-like protein Emit3 and the zinc-ribbon mutated Emit3","description":"Transposable elements (TEs) are threats to genome stability and thus small RNA-mediated heterochromatinization suppresses the transcription of TEs. Paradoxically, transcription of non-coding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) transcription machinery is required for such unconventional transcription in different organisms. Indeed, the developmental stage-specific Mediator complex (Med)-associated proteins play essential roles in the ncRNA transcription from TE-related sequences in Tetrahymena. Yet it remains unknown how those Med-associated proteins are linked to the TE transcription by Pol II. Here, have found that Pol II is regulated by Emit3, a stage-specific, TFIIB-like protein specialized in TE transcription. Hence, to find out potential interactions, we did LC-MS/MS analysis for immunoprecipitation samples of Emit3 and the zinc-ribbon mutated Emit3.","dates":{"publication":"2025-05-13","submission":"2024-11-06"},"accession":"PXD057568","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:485","NEWT:56636","NEWT:2499525","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52639","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1045775","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:1028307","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:441772","NEWT:1293091","NEWT:48106","NEWT:202956","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","N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