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- PDB-7o0u: Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o0u | ||||||||||||||||||||||||
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Title | Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A | ||||||||||||||||||||||||
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![]() | MEMBRANE PROTEIN / Photosynthesis / reaction centre light harvesting complex / RC-dLH / RC-LH1 / carotenoid / quinone / bacteriochlorophyll a / Gemmatimonas phototrophica | ||||||||||||||||||||||||
Function / homology | ![]() organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å | ||||||||||||||||||||||||
![]() | Qian, P. / Koblizek, M. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: 2.4-Å structure of the double-ring photosystem. Authors: Pu Qian / Alastair T Gardiner / Ivana Šímová / Katerina Naydenova / Tristan I Croll / Philip J Jackson / Nupur / Miroslav Kloz / Petra Čubáková / Marek Kuzma / Yonghui Zeng / Pablo ...Authors: Pu Qian / Alastair T Gardiner / Ivana Šímová / Katerina Naydenova / Tristan I Croll / Philip J Jackson / Nupur / Miroslav Kloz / Petra Čubáková / Marek Kuzma / Yonghui Zeng / Pablo Castro-Hartmann / Bart van Knippenberg / Kenneth N Goldie / David Kaftan / Pavel Hrouzek / Jan Hájek / Jon Agirre / C Alistair Siebert / David Bína / Kasim Sader / Henning Stahlberg / Roman Sobotka / Christopher J Russo / Tomáš Polívka / C Neil Hunter / Michal Koblížek / ![]() ![]() ![]() ![]() Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo- ...Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy. | ||||||||||||||||||||||||
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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 12.5 MB | Display | ![]() |
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Full document | ![]() | 13.4 MB | Display | |
Data in XML | ![]() | 190.4 KB | Display | |
Data in CIF | ![]() | 261.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12679MC ![]() 7o0vC ![]() 7o0wC ![]() 7o0xC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 12.1 TB Data #1: Unaligned multi-frame micrographs of RC-dLH1 complexes on HexAuFoil support [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 8 types, 46 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXCC1H1H2LM...
#1: Protein | Mass: 6061.153 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 38457.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 21079.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 7854.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | | Mass: 20022.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | | Mass: 30581.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | | Mass: 41182.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 7723.052 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein/peptide , 1 types, 40 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXbabbbcbdbebf...
#2: Protein/peptide | Mass: 5084.809 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 3 types, 127 molecules ![](data/chem/img/LMT.gif)
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#10: Polysaccharide | Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #12: Sugar | ChemComp-LMT / #16: Sugar | |
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-Non-polymers , 14 types, 682 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/V7N.gif)
![](data/chem/img/0V9.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/V75.gif)
![](data/chem/img/CD4.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/MQ8.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/V7B.gif)
![](data/chem/img/UYH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/V7N.gif)
![](data/chem/img/0V9.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/V75.gif)
![](data/chem/img/CD4.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/MQ8.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/V7B.gif)
![](data/chem/img/UYH.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | ChemComp-BCL / #13: Chemical | ChemComp-V7N / ( #14: Chemical | ChemComp-0V9 / ( #15: Chemical | ChemComp-HEC / #17: Chemical | #18: Chemical | ChemComp-CD4 / ( #19: Chemical | ChemComp-PGW / ( | #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-FE / | #23: Chemical | ChemComp-CRT / | #24: Chemical | #25: Chemical | ChemComp-UYH / [( | #26: 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: RC-dLH model_1a / Type: COMPLEX Details: Reaction centre light harvesting complex model_1a from Gemmatimonas phototrophic AP64 Entity ID: #1-#9 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 0.800 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||
Buffer solution | pH: 8 Details: The final purified complex is in 20mM Tris.Cl, 0.025 DDM, PH 8.0 buffer. | ||||||||||||
Buffer component |
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Specimen | Conc.: 6.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The protein complex was isolated from photosynthetic membrane using detergent beta-DDM. After purification, concentrated protein sample solution was stored in LN before using. | ||||||||||||
Specimen support | Details: plasma chamber (Fischione 1070) / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade | ||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Talmon type |
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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 / Nominal magnification: 120000 X / Nominal defocus max: -2400 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.2 sec. / Electron dose: 24.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 19865 Details: All movies were recorded from a HexAuFoil grid with a special EPU version, which can recognise 300 nm holes on the grid. |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1517482 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176531 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 30 / Protocol: FLEXIBLE FIT / Space: REAL / Details: ISOLDE incorporated in ChimeraX was used. | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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