+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32062 | |||||||||
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Title | Rba sphaeroides PufX-KO RC-LH1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem / Complex / PHOTOSYNTHESIS / Mutant | |||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rhodobacter sphaeroides 2.4.1 (bacteria) / Cereibacter sphaeroides 2.4.1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Bracun L / Yamagata A | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32062.map.gz | 55.7 MB | EMDB map data format | |
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Header (meta data) | emd-32062-v30.xml emd-32062.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32062_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_32062.png | 76.1 KB | ||
Filedesc metadata | emd-32062.cif.gz | 5.9 KB | ||
Others | emd_32062_additional_1.map.gz | 46.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32062 | HTTPS FTP |
-Validation report
Summary document | emd_32062_validation.pdf.gz | 697.7 KB | Display | EMDB validaton report |
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Full document | emd_32062_full_validation.pdf.gz | 697.3 KB | Display | |
Data in XML | emd_32062_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_32062_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32062 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32062 | HTTPS FTP |
-Related structure data
Related structure data | 7voyMC 7va9C 7vb9C 7vnmC 7vnyC 7vorC 7votC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32062.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_32062_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rhodobacter sphaeroides PufX-KO RC-LH1
+Supramolecule #1: Rhodobacter sphaeroides PufX-KO RC-LH1
+Macromolecule #1: Light-harvesting protein B-875 alpha chain
+Macromolecule #2: Light-harvesting protein B-875 beta chain
+Macromolecule #3: Reaction center protein L chain
+Macromolecule #4: Reaction center protein M chain
+Macromolecule #5: Reaction center protein H chain
+Macromolecule #6: BACTERIOCHLOROPHYLL A
+Macromolecule #7: BACTERIOPHEOPHYTIN A
+Macromolecule #8: UBIQUINONE-10
+Macromolecule #9: FE (II) ION
+Macromolecule #10: SPEROIDENONE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.549 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |