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Yorodumi- PDB-7vor: The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vor | ||||||||||||||||||||||||
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Title | The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1 | ||||||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / SUPERCOMPLEX / purple bacteria | ||||||||||||||||||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Cereibacter sphaeroides 2.4.1 (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||||||||||||||||||||
Authors | Cao, P. / Li, M. / Liu, L.N. | ||||||||||||||||||||||||
Funding support | China, United Kingdom, 7items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex. Authors: Peng Cao / Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tatsuki Negami / Baohua Zou / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Mei Li / Lu-Ning Liu / Abstract: The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species ...The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vor.cif.gz | 960 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vor.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vor_validation.pdf.gz | 5.7 MB | Display | wwPDB validaton report |
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Full document | 7vor_full_validation.pdf.gz | 5.8 MB | Display | |
Data in XML | 7vor_validation.xml.gz | 155.5 KB | Display | |
Data in CIF | 7vor_validation.cif.gz | 207.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7vor ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7vor | HTTPS FTP |
-Related structure data
Related structure data | 32058MC 7va9C 7vb9C 7vnmC 7vnyC 7votC 7voyC 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
-Reaction center protein ... , 3 types, 6 molecules LlMmHh
#1: Protein | Mass: 31477.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A5 #2: Protein | Mass: 34529.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A6 #3: Protein | Mass: 28066.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J170 |
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-Light-harvesting protein B-875 ... , 2 types, 56 molecules ADFIKOQSUW3179adfikoqsuw5b16b9BE...
#4: Protein | Mass: 6816.169 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A4 #5: Protein/peptide | Mass: 5592.361 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A3 |
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-Protein , 2 types, 4 molecules XxYy
#6: Protein | Mass: 9061.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: P13402 #7: Protein | Mass: 5555.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: ATH 2.4.1. / References: UniProt: U5NME9 |
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-Non-polymers , 7 types, 148 molecules
#8: Chemical | ChemComp-BCL / #9: Chemical | ChemComp-BPH / #10: Chemical | ChemComp-U10 / #11: Chemical | ChemComp-PC1 / #12: Chemical | #13: Chemical | ChemComp-SPO / #14: Chemical | ChemComp-CDL / |
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-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: The dimeric photosynthetic RC-LH1 supercomplex in Class1 Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL |
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Source (natural) | Organism: Cereibacter sphaeroides 2.4.1 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 2 mg/ml / 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 |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145392 / Symmetry type: POINT | ||||||||||||||||||||||||
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