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Yorodumi- PDB-7vzg: Structure of the Acidobacteria homodimeric reaction center bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vzg | ||||||
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Title | Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form) | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / membrane protein | ||||||
Function / homology | Function and homology information thylakoid / iron-sulfur cluster binding / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chloracidobacterium thermophilum (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å | ||||||
Authors | Huang, G.Q. / Dong, S.S. / Qin, X.C. / Sui, S.F. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c. Authors: Shishang Dong / Guoqiang Huang / Changhui Wang / Jiajia Wang / Sen-Fang Sui / Xiaochun Qin / Abstract: Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer ...Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 FeS clusters, 12 lipids, 2 Ca ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vzg.cif.gz | 497.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vzg.ent.gz | 401.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vzg_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7vzg_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7vzg_validation.xml.gz | 111.9 KB | Display | |
Data in CIF | 7vzg_validation.cif.gz | 149.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/7vzg ftp://data.pdbj.org/pub/pdb/validation_reports/vz/7vzg | HTTPS FTP |
-Related structure data
Related structure data | 32228MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 6 molecules AaCcBD
#1: Protein | Mass: 98537.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LDR8 #2: Protein | | Mass: 22369.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LDR4 #7: Protein | | Mass: 15664.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LDR3 #8: Protein | | Mass: 8199.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: A8DJF8 #9: Protein | | Mass: 8622.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LHG2 |
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-Protein/peptide , 4 types, 8 molecules EeFfGgHh
#3: Protein/peptide | Mass: 3684.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LK98 #4: Protein/peptide | Mass: 3885.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LEN5 #5: Protein/peptide | Mass: 4293.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) References: UniProt: G2LJ20 #6: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chloracidobacterium thermophilum (bacteria) |
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-Non-polymers , 12 types, 87 molecules
#10: Chemical | #11: Chemical | ChemComp-BCL / #12: Chemical | ChemComp-CLA / #13: Chemical | #14: Chemical | #15: Chemical | ChemComp-85I / [( #16: Chemical | ChemComp-UNL / Mass: 663.906 Da / Num. of mol.: 32 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION #17: Chemical | ChemComp-85N / [( #18: Chemical | #19: Chemical | #20: Chemical | #21: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: CabRC complex, the larger form / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: Chloracidobacterium thermophilum (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52612 / Symmetry type: POINT |