+Open data
-Basic information
Entry | Database: PDB / ID: 6nwa | |||||||||
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Title | The structure of the photosystem I IsiA super-complex | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem / Antenna / Chlorophyll / Membrane | |||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis ...plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Toporik, H. / Li, J. / Williams, D. / Chiu, P.L. / Mazor, Y. | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: The structure of the stress-induced photosystem I-IsiA antenna supercomplex. Authors: Hila Toporik / Jin Li / Dewight Williams / Po-Lin Chiu / Yuval Mazor / Abstract: Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with ...Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with antennae in vivo to increase the size of photosynthetic units to hundreds or thousands of pigments. Regulation of the interactions between antennae and photosystems allows photosynthetic organisms to adapt to their environment. In low-iron environments, cyanobacteria express IsiA, a PSI antenna, critical to their survival. Here we describe the structure of the PSI-IsiA complex isolated from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. This 2-MDa photosystem-antenna supercomplex structure reveals more than 700 pigments coordinated by 51 subunits, as well as the mechanisms facilitating the self-assembly and association of IsiA with multiple PSI assemblies. | |||||||||
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 | 6nwa.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6nwa.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6nwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nwa ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nwa | HTTPS FTP |
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-Related structure data
Related structure data | 0524MC 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, 6 molecules AaHBbG
#1: Protein | Mass: 83022.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I #2: Protein | Mass: 81369.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29255, photosystem I |
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-Protein , 2 types, 21 molecules CcNWXYZgynopqrhtuswxv
#3: Protein | Mass: 8837.261 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I #11: Protein | Mass: 37250.734 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55274 |
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-Photosystem I reaction center subunit ... , 8 types, 24 molecules DdOEePFfQIiRJjSLlUMmVkKT
#4: Protein | Mass: 15663.749 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P19569 #5: Protein | Mass: 8154.086 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P12975 #6: Protein | Mass: 18267.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29256 #7: Protein/peptide | Mass: 4414.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55330 #8: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55329 #9: Protein | Mass: 16631.795 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P37277 #10: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72986 #12: Protein | Mass: 8649.268 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72712 |
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-Sugars , 1 types, 3 molecules
#20: Sugar |
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-Non-polymers , 8 types, 768 molecules
#13: Chemical | ChemComp-LHG / #14: Chemical | ChemComp-LMG / #15: Chemical | #16: Chemical | ChemComp-CLA / #17: Chemical | ChemComp-PQN / #18: Chemical | ChemComp-SF4 / #19: Chemical | ChemComp-BCR / #21: Chemical | |
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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-IsiA / Type: COMPLEX / Details: PSI-IsiA from cyanobacteria / Entity ID: #1-#10 / Source: NATURAL |
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Molecular weight | Value: 2 MDa / Experimental value: NO |
Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 572000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74000 / Algorithm: BACK PROJECTION / Num. of class averages: 95 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 16.43 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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