+Open data
-Basic information
Entry | Database: PDB / ID: 7ew6 | ||||||
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Title | Barley photosystem I-LHCI-Lhca5 supercomplex | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / Light-harvesting complex / Lhca5 | ||||||
Function / homology | Function and homology information photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Hordeum vulgare subsp. spontaneum (wild barley) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Wang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Zhang, X. / Shen, J.R. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2022 Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang / Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET. #1: Journal: Science / Year: 2015 Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex Authors: Qin, X.C. / Suga, M. / Kuang, T.Y. / Shen, J.R. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ew6.cif.gz | 822.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ew6.ent.gz | 721.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ew6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ew6 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ew6 | HTTPS FTP |
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-Related structure data
Related structure data | 31348MC 7eu3C 7ewkC 7f9oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83217.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z1K7, photosystem I |
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#2: Protein | Mass: 82693.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z289, photosystem I |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFHIJKL
#4: Protein | Mass: 21958.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P36213 |
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#5: Protein | Mass: 15476.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P13194 |
#6: Protein | Mass: 24866.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P13192 |
#7: Protein | Mass: 14900.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P20143 |
#8: Protein/peptide | Mass: 4010.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z1D9 |
#9: Protein/peptide | Mass: 4747.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z1E9 |
#10: Protein | Mass: 13742.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P36886 |
#11: Protein | Mass: 22229.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: P23993 |
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 15
#12: Protein | Mass: 26691.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: A0A287WC32 |
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#15: Protein | Mass: 27618.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
-Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 23
#13: Protein | Mass: 27320.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: Q43485 |
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#14: Protein | Mass: 29374.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: F2DAN8 |
-Protein / Sugars , 2 types, 3 molecules C
#22: Sugar | #3: Protein | | Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4YZ47, photosystem I |
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-Non-polymers , 10 types, 197 molecules
#16: Chemical | ChemComp-CL0 / | ||||||||||||||||
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#17: Chemical | ChemComp-CLA / #18: Chemical | #19: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-BCR / #21: Chemical | #23: Chemical | ChemComp-LMG / #24: Chemical | ChemComp-LUT / ( #25: Chemical | ChemComp-CHL / #26: Chemical | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PSI-LHCI-Lhca5 supercomplex of Barley / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL |
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Source (natural) | Organism: Hordeum vulgare subsp. spontaneum (wild barley) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT |