+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30656 | ||||||||||||||||||
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Title | Structure of RC-LH1-PufX from Rhodobacter veldkampii | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | membrane protein / light-harvesting / reaction center / pufx / PHOTOSYNTHESIS | ||||||||||||||||||
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 / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Rhodobacter veldkampii DSM 11550 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||||||||
Authors | Bracun L / Yamagata A | ||||||||||||||||||
Funding support | United Kingdom, Japan, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30656.map.gz | 51.7 MB | EMDB map data format | |
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Header (meta data) | emd-30656-v30.xml emd-30656.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30656_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_30656.png | 176.7 KB | ||
Masks | emd_30656_msk_1.map | 67 MB | Mask map | |
Filedesc metadata | emd-30656.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30656 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30656 | HTTPS FTP |
-Validation report
Summary document | emd_30656_validation.pdf.gz | 551.9 KB | Display | EMDB validaton report |
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Full document | emd_30656_full_validation.pdf.gz | 551.5 KB | Display | |
Data in XML | emd_30656_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_30656_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30656 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30656 | HTTPS FTP |
-Related structure data
Related structure data | 7ddqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30656.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_30656_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosynthetic core complex featuring reaction center, LH1 and PufX
+Supramolecule #1: Photosynthetic core complex featuring reaction center, LH1 and PufX
+Macromolecule #1: Antenna pigment protein alpha chain
+Macromolecule #2: Antenna pigment protein beta chain
+Macromolecule #3: PufX
+Macromolecule #4: Photosynthetic reaction center L subunit
+Macromolecule #5: Reaction center protein M chain
+Macromolecule #6: Photosynthetic reaction center subunit H
+Macromolecule #7: BACTERIOCHLOROPHYLL A
+Macromolecule #8: SPHEROIDENE
+Macromolecule #9: UBIQUINONE-10
+Macromolecule #10: BACTERIOPHEOPHYTIN A
+Macromolecule #11: FE (III) ION
+Macromolecule #12: 1,2-Distearoyl-sn-glycerophosphoethanolamine
-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 / Material: COPPER / Mesh: 300 / 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 (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |