+Open data
-Basic information
Entry | Database: PDB / ID: 7ddq | ||||||||||||||||||
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Title | Structure of RC-LH1-PufX from Rhodobacter veldkampii | ||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / membrane protein / light-harvesting / reaction center / pufx | ||||||||||||||||||
Function / homology | Function and homology information organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Rhodobacter veldkampii DSM 11550 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||||||||
Authors | Bracun, L. / Yamagata, A. / Shirouzu, M. / Liu, L.N. | ||||||||||||||||||
Funding support | United Kingdom, Japan, 5items
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Citation | Journal: Sci Adv / Year: 2021 Title: Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution. Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Lu-Ning Liu / Abstract: The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for ...The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo-electron microscopy structure of the RC-LH1-PufX supercomplex from at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular "cross brace" to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation. | ||||||||||||||||||
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 | 7ddq.cif.gz | 493.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ddq.ent.gz | 423 KB | Display | PDB format |
PDBx/mmJSON format | 7ddq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/7ddq ftp://data.pdbj.org/pub/pdb/validation_reports/dd/7ddq | HTTPS FTP |
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-Related structure data
Related structure data | 30656MC 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
-Antenna pigment protein ... , 2 types, 30 molecules otraebkfusnijgdNSOUDAJETRKGIFB
#1: Protein | Mass: 6699.024 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIR4 #2: Protein/peptide | Mass: 5551.439 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIL7 |
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-Protein , 2 types, 2 molecules XM
#3: Protein | Mass: 8923.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIP3 |
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#5: Protein | Mass: 34425.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIN0 |
-Photosynthetic reaction center ... , 2 types, 2 molecules LH
#4: Protein | Mass: 30896.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIS6 |
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#6: Protein | Mass: 27445.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Rhodobacter veldkampii DSM 11550 (bacteria) References: UniProt: A0A2T4JIP4 |
-Non-polymers , 6 types, 62 molecules
#7: Chemical | ChemComp-BCL / #8: Chemical | ChemComp-SPO / #9: Chemical | ChemComp-U10 / #10: Chemical | #11: Chemical | ChemComp-FE / | #12: Chemical | |
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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: Photosynthetic core complex featuring reaction center, LH1 and PufX Type: COMPLEX / Entity ID: #3-#6 / Source: NATURAL |
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Source (natural) | Organism: Rhodobacter veldkampii DSM 11550 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
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: DARK FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184921 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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