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Open data
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Basic information
Entry | Database: PDB / ID: 6z5r | ||||||
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Title | RC-LH1(16) complex from Rhodopseudomonas palustris | ||||||
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![]() | PHOTOSYNTHESIS / Reaction center / Light harvesting / Protein W / Quinone | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Swainsbury, D.J.K. / Qian, P. / Hitchcock, A. / Hunter, C.N. | ||||||
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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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 543.3 KB | Display | ![]() |
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PDB format | ![]() | 493.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 131.6 KB | Display | |
Data in CIF | ![]() | 157.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11080MC ![]() 6z5sC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Light-harvesting complex 1 ... , 2 types, 32 molecules CEGJNRTVPYA13579DFIKOSUXQZB24680
#1: Protein/peptide | Mass: 5779.999 Da / Num. of mol.: 16 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-98 / CGA009 / References: UniProt: Q6N9L4 #2: Protein | Mass: 5849.797 Da / Num. of mol.: 16 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-98 / CGA009 / References: UniProt: Q6N9L5 |
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-Reaction center protein ... , 2 types, 2 molecules LM
#4: Protein | Mass: 30857.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-98 / CGA009 / References: UniProt: O83005 |
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#5: Protein | Mass: 34453.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-98 / CGA009 / References: UniProt: A0A4Z7 |
-Protein / Sugars , 2 types, 13 molecules H![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#10: Sugar | ChemComp-LMT / #3: Protein | | Mass: 27268.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-98 / CGA009 / References: UniProt: A0A4Z9 |
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-Non-polymers , 10 types, 96 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/6PL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/QAK.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/6PL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/QAK.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-BCL / #7: Chemical | ChemComp-CRT / #8: Chemical | ChemComp-6PL / ( #9: Chemical | ChemComp-CDL / #11: Chemical | #12: Chemical | ChemComp-U10 / #13: Chemical | ChemComp-FE / | #14: Chemical | ChemComp-QAK / ( | #15: Chemical | #16: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Reaction center-Light harvesting complex 1 / Type: COMPLEX Details: Reaction center-Light harvesting complex 1 from Rhodopseudomonas palustris Entity ID: #1-#5 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 3.52 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() Cellular location: Lamellar membranes | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 60 % / Chamber temperature: 298 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 55.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 476547 / Details: Autopicked in RELION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260752 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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