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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11080 | |||||||||
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Title | RC-LH1(16) complex from Rhodopseudomonas palustris | |||||||||
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Function / homology | ![]() 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 / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Swainsbury DJK / Qian P / Hitchcock A / Hunter CN | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of RC-LH1 complexes with open or closed quinone channels. Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / ...Authors: David J K Swainsbury / Pu Qian / Philip J Jackson / Kaitlyn M Faries / Dariusz M Niedzwiedzki / Elizabeth C Martin / David A Farmer / Lorna A Malone / Rebecca F Thompson / Neil A Ranson / Daniel P Canniffe / Mark J Dickman / Dewey Holten / Christine Kirmaier / Andrew Hitchcock / C Neil Hunter / ![]() ![]() ![]() Abstract: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes ...The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from A 2.65-Å resolution structure of the RC-LH1-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 57.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z5rMC ![]() 6z5sC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Reaction center-Light harvesting complex 1
+Supramolecule #1: Reaction center-Light harvesting complex 1
+Macromolecule #1: Light-harvesting complex 1 alpha chain
+Macromolecule #2: Light-harvesting complex 1 beta chain
+Macromolecule #3: H subunit of photosynthetic reaction center complex
+Macromolecule #4: Reaction center protein L chain
+Macromolecule #5: Reaction center protein M chain
+Macromolecule #6: BACTERIOCHLOROPHYLL A
+Macromolecule #7: SPIRILLOXANTHIN
+Macromolecule #8: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...
+Macromolecule #9: CARDIOLIPIN
+Macromolecule #10: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #11: BACTERIOPHEOPHYTIN A
+Macromolecule #12: UBIQUINONE-10
+Macromolecule #13: FE (III) ION
+Macromolecule #14: (6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,1...
+Macromolecule #15: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #16: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: LEICA EM GP | ||||||||||||
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | ![]() PDB-6z5r: |