{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/checksum.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_SP_PT1.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_PT3.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_SP_P2.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_P2.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_PT1.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_SP_PT2.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_PT2.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_P1.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_SP_P1.csv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/proteins_GPI_P3.csv"],"Mzxml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_PT1_6838.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_P1_6839.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_PT2_6842.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_P3_6833.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_P2_6840.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/SP_PT2_6837.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/SP_PT1_6841.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/SP_P1_6834.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/SP_P2_6836.mzXML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD048337/GPI_PT3_6832.mzXML"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["hafidh@ueb.cas.cz"],"submitter":["Petr Pompach"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Eif3","Phosphorylation","Translation initiation","Proteosome","Polarity","Pollen tube","Pci domain","Ribosome profiling","Ripseq"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD048337"],"sample_protocol":["Samples were digested by trypsin O/N at 37°C and analyzed using a liquid chromatography system Vanquish (Thermo Scientific) connected to the timsToF SCP mass spectrometer equipped with Captive spray (Bruker Daltonics). Mass spectrometer was operate in a positive data-dependent mode. One microliters of peptide mixture were injected by autosampler on the C18 trap column (Pepmap Neo C18 5µm, 0.3 x 5 mm, Thermo Scientific). After trapping, peptides were elute from the trap column and separated on a C18 column (Pepsep C18 150 x 0.15 mm, 1.5 µm, Bruker Daltonics) by a linear 35 min water−acetonitrile gradient from 5% (v/v) to 35% (v/v) acetonitrile at a flow rate of 1.5µL/min. The trap and analytical columns were both heat to 50°C. Parameters from the standard proteomics PASEF method were use to set timsTOF SCP. The target intensity per individual PASEF precursor was set to 20000, and the intensity threshold was set to 1500. The scan range was set between 0.6 and 1.6 V s/ cm2 with a ramp time of 100 ms. The number of PASEF MS/MS scans was 10. Precursor ions in the m/z range between 100 and 1700 with charge states ≥2+ and ≤6+ were select for fragmentation. The active exclusion was enable for 0.4 min."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The raw data were process by PeaksStudio 10.0 software (Bioinformatics Solutions, Canada). The search parameters were set as follows: enzyme – trypsin (semispecific), carbamidomethylation as a fixed modification, oxidation of methionine and acetylation of protein N-terminus as variable modifications. The data were search against the Arabidopsis thaliana protein database."],"omics_type":["Proteomics"],"labhead":["Said Hafidh"],"instrument_platform":[""],"labhead_affiliation":["Laboratory of Pollen Biology, Lab 105 Institute of Experimental Botany (IEB ASCR) Czech Republic"],"submission_type":["PARTIAL"],"species":["Nicotiana Tabacum (common Tobacco)"],"submitter_mail":["petr.pompach@ibt.cas.cz"],"publication":["41701515 Kumar V, Merret R, Carpentier MC, Honys D, Hafidh S. Domain architecture of plant eukaryotic translation initiation factor 3 subunit E governs interaction with translational cis-elements to regulatepollen tube growth. Plant Cell. 2026 38(2):koag005 10.1093/plcell/koag005"],"submitter_affiliation":["Intitute of Biotechnology"],"submitter_country":["Czechia"],"pubmed_abstract":["An octameric eukaryotic translation initiation factor 3 subunit E (eIF3E) preserves translational homeostasis through selective messenger RNA (mRNA) recognition and ribosome assembly. Yet, the mechanisms by which eIF3E maintains translational equilibriumremain poorly understood. We show here that eIF3E domain architecture and phosphorylation sites (Thr417, Ser421) are conserved across eukaryotes. Deleting the Proteasome-COP9 signalosome-Initiation factor 3 domain (PCI domain) abolished nuclear localization, disrupted eIF3E-eIF3L interaction, and impaired eIF3E dissociation from the polysomes. Affnity RNA immunoprecipitation sequencing of eIF3E::YFP in tobacco pollen tubes identified mRNAs bearing coding-sequence motifs (MC1 to MC3) that co-immunoprecipitate with eIF3E.Using mRNA reporter assay, we reveal that these motifs act in tandem as eIF3E-dependent translational repressors and enhancers. AlphaFold3 structural modeling and Förster resonance energy transfer verification indicate that PCI domain deletion or PCI-phosphosite mutagenesis weaken eIF3E-eIF3L interactions and block translational activation of MC2 RNA reporter. We further show thatloss of the PCI domain or PCI-phosphosite mutagenesis misregulate pollen tube growth and membrane organization. Together, our findings underscore eIF3E as a selective regulator of mRNA translation that couplescis-motifrecognition to membrane integrityand pollen tube growth, thereby ensuringplant fertility."],"pubmed_title":["Domain architecture of plant eukaryotic translation initiation factor 3 subunit E governs interaction with translational cis-elements to regulatepollen tube growth."],"pubmed_authors":["Kumar Vinod V, Merret Rémy R, Carpentier Marie C MC, Honys David D, Hafidh Said S"],"additional_accession":[]},"is_claimable":false,"name":"Domains architecture and phospho-switches of eIF3e translation subunit control pollen tube growth and morphology","description":"The eIF3e subunit form an octameric ribonucleoprotein complex to initiate translation, and its PCI domain engage in the assembly of the proteolytic 26S proteosome supercomplex. These two complexes are central in translation initiation and protein quality surveillance and turnover. However, how eIF3e is structurally regulated remain unknown. Here, using RIPseq approach we revealed that eIF3e co-immunoprecipitate with mRNAs involved in RNA biosynthesis (U3 snRNA12a and ncRNA processing) and cell morphology, and its PCI domain is crucial for regulation of pollen tube pulse growth and eIF3e dissociation post initiation. We show that motifs within eIF3e associated target RNAs can repress or activate translation. Since the PCI domain associate with the proteosome machinery, we show that pharmacological inhibition of the proteosome complex accumulate eIF3e, eIF3eΔPCI and the proteosome lid subunits RPN7/RPN12a to the nucleus and generate nuclear condensates. Importantly, constitutive dephosphorylation of eIF3e revealed antagonistic phosphosites at the PCI domain that balance pollen tube growth and cellular membrane morphology. These findings inform structural features that control eIF3e activities and that antagonistic de-phosphorylation of eIF3e maintain equilibrium of pollen tube growth rate dynamics and membrane structural morphology.","dates":{"publication":"2026-04-06","submission":"2024-01-09"},"accession":"PXD048337","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:588858","NEWT:9639","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:2172103","NEWT:7460","NEWT:6491","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NE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