Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

XL-MS Characterization of spinach Photosystem II Assembly

ABSTRACT: Cross-linking mass spectrometry was used to determine the collective binding/stabilization of the TLP18.3 and Psb27 proteins to the luminal PSII CP43 protein. This pipeline also discovered the structural location of a Rubredoxin protein on the stromal side of PSII.

INSTRUMENT(S):

ORGANISM(S): Spinacia Oleracea

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Youngwoo Lee

LAB HEAD: Haijun Liu

PROVIDER: PXD073794 | Pride | 2026-04-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	073015_BBY_C01_01.raw	Raw
	073015_BBY_C01_02.raw	Raw
	073015_BBY_X01_01.raw	Raw
	073015_BBY_X01_02.raw	Raw
	080615_BBY_Plus3DDA_01.raw	Raw

Items per page:

1 - 5 of 15

Publications

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and rubredoxin-ENH1 to the stromal side of photosystem II in higher plants.

Liu Haijun H Lee Youngwoo Y

The Journal of biological chemistry 20260310 5

Thylakoid lumen protein 18.3 and Psb27 are known proteins on the luminal side of photosystem II (PSII). The structural locations of these two proteins are still absent in the currently available higher plant PSII cryogenic electron microscopy structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by LC-MS/MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modeling to determine the collectiv ...[more]

PMID: 41819263

Similar Datasets

Chemical crosslinking of photosystem I antenna proteins

Project description:Chemical crosslinking (DSS) of proteins in conjunction with mass spectrometry was performed to identify protein-protein interactions between the light-harvesting proteins of PSI and PSII.

2025-04-29 | PXD051493 | Pride

How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by integrative structural mass-spectrometry

Project description:Photosynthesis drives all life on Earth by exploiting solar energy to split water molecules through the Photosystem (PS) II enzyme. In plant thylakoid membranes, PSII binds a modular set of light harvesting complexes (LHCII) to form different types of PSII-LHCII supercomplex (PSII-LHCIIsc). Plant PSII-LHCIIsc are localized in the stacked region of the thylakoid membranes called grana, from which they can be isolated in paired conformations of type (C2S2M2)x2 and (C2S2M)x2, with the two supercomplexes facing each other at their stromal surface. Although the atomic structure of PSII-LHCIIsc has recently been solved, there is still a lack of knowledge on their mutual interactions when facing each other within apposing thylakoid membranes, as well as their structural dynamics in response to light variations. The major challenges in the structural determination of the stromal interactions are posed not only by the dynamic nature of these over 2-megadalton assemblies, but also by the heterogeneity of the LHCII subunits and the high flexibility of their stromally exposed N-terminal loops. Here, we explored the potential of combining top-down mass spectrometry (TD-MS) and crosslinking mass spectrometry (XL-MS) to peek through the keyhole of the tight stromal gap between two facing supercomplexes, unveiling so far hidden structural details. A first goal of experiments was to identify the distinct sequence variants and proteoforms involved in PSII-LHCIIsc structural dynamics in response to light modulation. To investigate their structural interactions, we treated paired PSII-LHCIIsc isolated from the three light conditions with two complementary chemical cross-linkers, targeting different residues and producing partially overlapping distance restraints. Most interactions detected “in-vitro” on the isolated paired supercomplexes were further supported by XL-MS results obtained “in-situ” on the corresponding thylakoid membranes.

2020-03-19 | PXD017382 | Pride

Xilmass: a new approach towards the identification of cross-linked peptides

Project description:Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in a novel way in the search database that explicitly encodes cross-linking sites and (ii) the scoring function from the Andromeda algorithm was adapted to score against a theoretical MS spectrum that contains the peaks from all the possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was subsequently evaluated against the recently published Kojak and the popular pLink algorithms on a data set that contains calmodulin-plectin.

2016-09-27 | PXD003880 | Pride

Structure of Cyanobacterial Phycobilisome Core Revealed by Structural Modeling and Chemical Cross-linking

Project description:In cyanobacteria and red algae, the structural basis dictating efficient excitation energy transfer from the phycobilisome (PBS) antenna complex to the reaction centers (RCs) remains unclear. PBS has several peripheral rods and a central core, which binds to the thylakoid membrane, allowing energy coupling with Photosystems II (PSII) and Photosystem I (PSI). Here, we integrated chemical cross-linking mass spectrometry with homology modeling analysis to propose a tri-cylindrical cyanobacterial PBS-core structure. Our model reveals a side view crossover configuration of the two basal cylinders, consolidating the essential roles of the anchoring domains comprised of the ApcE PB-loop and ApcD, which facilitate the energy transfer to PSII and PSI respectively. The uneven bottom surface of the PBS-core contrasts with the flat reducing side of PSII. The extra space between two basal cylinders of the PBS-core and PSII provides increased accessibility of regulatory elements, e.g., orange carotenoid protein, which are required for modulating photochemical activities.

2021-09-09 | PXD017873 | Pride

Unique organization of photosystem II supercomplexes and megacomplexes in Norway spruce.

Project description:Photosystem II (PSII) complexes are organized into large supercomplexes with variable amounts of light-harvesting proteins (Lhcb). A typical PSII supercomplex in plants is formed by four trimers of Lhcb proteins (LHCII trimers), which are bound to the PSII core dimer via monomeric antenna proteins. However, the architecture of PSII supercomplexes in Norway spruce (Picea abies (L.) Karst.) is different, most likely due to a lack of two Lhcb proteins, Lhcb6 and Lhcb3. Interestingly, the spruce PSII supercomplex shares similar structural features with its counterpart in the green alga Chlamydomonas reinhardtii (Kouřil et al.: New Phytol. 210, 808-814, 2016). Here we present a single-particle electron microscopy study of isolated PSII supercomplexes from Norway spruce that revealed binding of a variable amount of LHCII trimers to the PSII core dimer at positions that have never been observed in any other plant species so far. The largest spruce PSII supercomplex, which was found to bind 8 LHCII trimers, is even larger than the current largest known PSII supercomplex from Chlamydomonas reinhardtii. We have also shown that the spruce PSII supercomplexes can form various types of PSII megacomplexes, which were also identified in intact grana membranes. Some of these large PSII supercomplexes and megacomplexes were identified also in Pinus sylvestris, another representative of Pinaceae family. The structural variability and complexity of LHCII organization in Pinaceae seems to be related to the absence of Lhcb6 and Lhcb3 in this family and may be beneficial for the optimization of light-harvesting under varying environmental conditions.

2021-09-09 | PXD020138 | Pride

Cryo-EM structure of photosystem II supercomplex from Chlorella ohadii, a green microalga with extreme phototolerance

Project description:Photosystem II (PSII) is essential for energy conversion during oxygenic photosynthesis in plants and algae. Chlorella ohadii, one of the fastest multiplying green alga, thrives under the harsh desert sun but lacks the standard PSII photoprotective mechanisms involving LhcSR/PsbS proteins or protein phosphorylation. Here, we present analysis of cryo-EM structure of the PSII supercomplex from C. ohadii at 2.9Å resolution to determine whether the exceptional resistance to desert conditions has a structural basis in PSII. The structure reveals a novel PsbO isoform and additional subunits, PsbR and PsbY, which enhance core complex stability through extensive interactions. Furthermore, the trimeric light-harvesting complexes (LHCII) are bound to the PSII core by specific light-harvesting proteins whose down-regulation in response to high light conditions implies a reduction in the number of bound LHCII trimers. These modifications play a crucial role in maintaining PSII stability and photoprotection, allowing C. ohadii to survive in extreme conditions.

2025-10-06 | PXD059509 | Pride

Identification of proteins in separated PSII supercomplexes from spruce (P. abies)

Project description:To identify protein composition of photosystem II (PSII) supercomplexes separated from spruce seedlings using sucrose gradient centrifugation. These supercomplexes represent mainly so called C2S2 PSII supercomplex as revealed by high-resolution cryo-EM.

2023-07-19 | PXD035272 | Pride

A unique photoprotection mechanism in Chlorella species

Project description:Light is the driving force of photosynthesis. However, excessive light can be harmful. Photoinhibition, or lightinduced photodamage, is one of the key processes limiting photosynthesis. When the absorbed light exceeds the amount that can be dissipated by photosynthetic electron flow and other processes, damaging radicals are formed that mostly inactivate photosystem II (PSII). A welldefined mechanism that protects the photosynthetic apparatus from photoinhibition has been described in the model green alga Chlamydomonas reinhardtii and plants. Chlorella ohadii is a green microalga, isolated from biological desert soil crusts, that thrives under extreme high light (HL) in which other organisms do not survive. Here, we show that this alga evolved unique protection mechanisms distinct from those of C. reinhardtii and plants. When grown under extreme HL, significant structural changes were noted in the C. ohadii thylakoids, including a drastic reduction in the antennae and the formation of stripped core PSII, lacking its outer and inner antennae. This is accompanied by a massive accumulation of protective carotenoids and proteins that scavenge harmful radicals. At the same time, several elements central to photoinhibition protection in C. reinhardtii, such as psbS, the stressrelated light harvesting complex (LHCSR), PSII protein phosphorylation and statetransitions are entirely absent or were barely detected in C. ohadii. A carotenoid biosynthesis related protein (CBR) is largely accumulated in the LHCII remains of HL cells and in the absence of psbS and LHCSR can function in sensing the HL and protecting from PI. Taken together, a unique photoinhibition protection mechanism evolved in C. ohadii, enabling the species to thrive under extremelight intensities where other photosynthetic organisms fail to survive.

2023-05-08 | PXD038704 | Pride

Structural and functional differentiation of the light-harvesting protein Lhcb4 during land plant diversification

Project description:About 475 million years ago plants originated from an ancestral green alga and evolved first as non-vascular and later as vascular plants, becoming the primary producers of biomass on lands. During that time, the light harvesting complex II (LHCII), responsible for sunlight absorption and excitation energy transfer to the Photosystem II (PSII) core, underwent extensive differentiation. Lhcb4 is an ancestral ubiquitous LHCII that during plant diversification continued to change, finally differentiating in flowering plants in up to three isoforms, Lhcb4.1, Lhcb4.2 and Lhcb4.3. The pivotal position of Lhcb4 in the PSII-LHCII supercomplex (PSII-LHCIIsc), as linker for S- and M-trimers of LHCII to the PSII core, suggests its major role in light harvesting modulation. The increased accumulation of Lhcb4.3 observed in PSII-LHCIIsc of plants acclimated to moderate and high light intensities induced us to investigate whether this isoform is present in a specific PSII-LHCIIsc conformation that might explain its light-dependent accumulation. In this work, by combining an improved method for separation of different forms of PSII-LHCIIsc from thylakoids of Pisum sativum grown at increasing irradiances with quantitative proteomics, we assessed that Lhcb4.3 is abundant in PSII-LHCIIsc of type C2S2, irrespective of the plant growth irradiance. Phylogenetic comparative analysis on different taxa of the Viridiplantae lineage and structural modelling further pointed out to an effect of the evolution of different Lhcb4 isoforms on the light-dependent modulation of the PSII-LHCIIsc organization. This information provides new insight on the properties of the Lhcb4 and its isoforms and their role on the structure, function and regulation of PSII.

2019-03-25 | PXD011213 | Pride

Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry

Project description:Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2 - S3 and S3 - S4 - S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

2025-05-07 | PXD061921 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data