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Open data
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Basic information
Entry | Database: PDB / ID: 6et5 | ||||||
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Title | Reaction centre light harvesting complex 1 from Blc. virids | ||||||
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![]() | PHOTOSYNTHESIS / Reaction centre light harvesting complex 1 Blc. viridis Cryo-EM RC-LH1 Photosynthesis | ||||||
Function / homology | ![]() light-harvesting complex / 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 / photosynthesis ...light-harvesting complex / 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 / photosynthesis / membrane => GO:0016020 / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å | ||||||
![]() | Qian, P. / Siebert, C.A. / Canniffe, D.P. / Wang, P. / Hunter, C.N. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Authors: Pu Qian / C Alistair Siebert / Peiyi Wang / Daniel P Canniffe / C Neil Hunter / ![]() Abstract: The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the ...The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the bacteriochlorophyll b-based LH1-RC complex from Blastochloris viridis that reveals the structural basis for absorption of infrared light and the molecular mechanism of quinone migration across the LH1 complex. The triple-ring LH1 complex comprises a circular array of 17 β-polypeptides sandwiched between 17 α- and 16 γ-polypeptides. Tight packing of the γ-apoproteins between β-polypeptides collectively interlocks and stabilizes the LH1 structure; this, together with the short Mg-Mg distances of bacteriochlorophyll b pairs, contributes to the large redshift of bacteriochlorophyll b absorption. The 'missing' 17th γ-polypeptide creates a pore in the LH1 ring, and an adjacent binding pocket provides a folding template for a quinone, Q , which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc complex. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 787.6 KB | Display | ![]() |
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PDB format | ![]() | 681.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3951MC 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
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 37179.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: reaction centre cytochrome subunit / Source: (natural) ![]() |
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-Reaction center protein ... , 3 types, 3 molecules LMH
#2: Protein | Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: reaction centre L subunit / Source: (natural) ![]() |
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#3: Protein | Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Teaction centre M subunit / Source: (natural) ![]() |
#4: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Reaction centre H subunit / Source: (natural) ![]() |
-Light-harvesting protein B-1015 ... , 3 types, 50 molecules zFKPSVYbehknqtw361GNQTWZcfilor...
#5: Protein | Mass: 6984.262 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Details: Light harvesting complex 1 alpha subunit / Source: (natural) ![]() #6: Protein | Mass: 6274.327 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Details: Light harvesting complex 1 beta subunit / Source: (natural) ![]() #7: Protein/peptide | Mass: 2799.292 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Details: Light harvesting complex 1 gamma subunit / Source: (natural) ![]() |
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-Non-polymers , 10 types, 75 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/MQ9.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/NS0.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/UQ9.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/MQ9.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/NS0.gif)
#8: Chemical | ChemComp-HEM / #9: Chemical | ChemComp-BCB / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-FE / | #13: Chemical | ChemComp-SO4 / #14: Chemical | #15: Chemical | ChemComp-MQ9 / | #16: Chemical | ChemComp-NS5 / | #17: Chemical | ChemComp-NS0 / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Reaction centre-Light harvesting complex 1 (RC-LH1) / Type: COMPLEX Details: The protein was isolated from a photosynthetic bacterium Blc. viridis. Entity ID: #1-#7 / Source: NATURAL |
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Molecular weight | Value: 0.414 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.8 / Details: 20 mMol HEPES, pH 7.8, 100 mM NaCl |
Buffer component | Conc.: 20 mMol / Name: HEPES |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Protein was solubilised by the use detergent of beta-DDM. The protein particle therefore contains a detergent belt in its hydrophobic region. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Temp: 277 K / Humidity: 99 % / Chamber temperature: 278 K Details: Blot for 3.5 seconds. Humidity: 99% Temperature:4C. |
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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 / Calibrated magnification: 130000 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 77 K |
Image recording | Average exposure time: 0.5 sec. / Electron dose: 2.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6472 |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
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Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Dose fractioned | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: gctf was used for CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 267726 / Details: Protein was checked using negatively stained EM. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267726 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3→243.8 Å / Cor.coef. Fo:Fc: 0.875 / SU B: 12.39 / SU ML: 0.188 / ESU R: 0.189 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 153.894 Å2
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Refinement step | Cycle: 1 / Total: 31896 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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