+Open data
-Basic information
Entry | Database: PDB / ID: 7vd5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of C2S2M2-type PSII-FCPII supercomplex from diatom | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / Photosystem / PSII | ||||||
Function / homology | Function and homology information light-harvesting complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II stabilization / photosystem II reaction center / : / thylakoid / photosynthetic electron transport chain / response to herbicide ...light-harvesting complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II stabilization / photosystem II reaction center / : / thylakoid / photosynthetic electron transport chain / response to herbicide / photosystem II / plastid / extrinsic component of membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / membrane => GO:0016020 / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetoceros gracilis (Diatom) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Nagao, R. / Kato, K. / Akita, F. / Miyazaki, N. / Shen, J.R. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex Authors: Nagao, R. / Kato, K. / Kumazawa, M. / Ifuku, K. / Yokono, M. / Suzuki, T. / Dohmae, N. / Akita, F. / Akimoto, S. / Miyazaki, N. / Shen, J.R. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7vd5.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vd5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vd5_validation.pdf.gz | 24 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vd5_full_validation.pdf.gz | 25.4 MB | Display | |
Data in XML | 7vd5_validation.xml.gz | 601.5 KB | Display | |
Data in CIF | 7vd5_validation.cif.gz | 710.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vd5 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vd5 | HTTPS FTP |
-Related structure data
Related structure data | 31905MC 7vd6C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Photosystem II ... , 15 types, 30 molecules AaBbCcDdHhIiJjKkLlMmTtYyXxZzWw
#1: Protein | Mass: 37036.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C261 #2: Protein | Mass: 53762.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E3 #3: Protein | Mass: 49468.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVV7 #4: Protein | Mass: 37983.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C012 #7: Protein | Mass: 7287.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7XBY7 #8: Protein/peptide | Mass: 4069.853 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT8 #9: Protein/peptide | Mass: 3589.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C298 #10: Protein/peptide | Mass: 4220.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BWI3 #11: Protein/peptide | Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C262 #12: Protein/peptide | Mass: 4473.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C2A0 #14: Protein/peptide | Mass: 3554.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E6 #17: Protein/peptide | Mass: 3609.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT2 #18: Protein/peptide | Mass: 3772.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF2 #19: Protein | Mass: 6328.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C215 #21: Protein | Mass: 5944.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E8 |
---|
-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 8687.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C209 #6: Protein/peptide | Mass: 3207.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT0 |
---|
-Extrinsic protein in photosystem ... , 3 types, 6 molecules OoUuQq
#13: Protein | Mass: 26419.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE8 #15: Protein | Mass: 10137.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF0 #20: Protein | Mass: 16731.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE9 |
---|
-Protein , 7 types, 14 molecules Vv123216361737193920402141
#16: Protein | Mass: 14780.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF4 #25: Protein | Mass: 18525.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #29: Protein | Mass: 19620.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #30: Protein | Mass: 19202.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #32: Protein | Mass: 24681.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #33: Protein | Mass: 16968.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #34: Protein | Mass: 17888.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
---|
-Unknown protein ... , 2 types, 4 molecules 0516
#22: Protein/peptide | Mass: 2656.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) #23: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
---|
-Chlorophyll a/b-binding ... , 5 types, 10 molecules 11311333143415351838
#24: Protein | Mass: 19109.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 #26: Protein | Mass: 18448.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 #27: Protein | Mass: 18768.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 #28: Protein | Mass: 18596.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 #31: Protein | Mass: 18351.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6 |
---|
-Sugars , 2 types, 10 molecules
#44: Sugar | ChemComp-DGD / #51: Sugar | |
---|
-Non-polymers , 16 types, 590 molecules
#35: Chemical | #36: Chemical | #37: Chemical | ChemComp-CLA / #38: Chemical | ChemComp-PHO / #39: Chemical | ChemComp-BCR / #40: Chemical | ChemComp-SQD / #41: Chemical | ChemComp-LMG / #42: Chemical | #43: Chemical | ChemComp-LHG / #45: Chemical | ChemComp-PL9 / #46: Chemical | ChemComp-HEM / #47: Chemical | ChemComp-KC1 / #48: Chemical | ChemComp-A86 / ( #49: Chemical | ChemComp-UNL / Num. of mol.: 38 / Source method: obtained synthetically #50: Chemical | ChemComp-DD6 / ( #52: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|---|
Sequence details | Authors do not know the sequences for chain 0, 1, 5, and 6. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C2S2M2-type PSII-FCPII supercomplex / Type: COMPLEX / Entity ID: #1-#30 / Source: NATURAL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.15 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Chaetoceros gracilis (Diatom) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
| ||||||||||||
Specimen | Conc.: 0.256 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8093924 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210825 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6J40 |