+Open data
-Basic information
Entry | Database: PDB / ID: 6m32 | ||||||
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Title | Cryo-EM structure of FMO-RC complex from green sulfur bacteria | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosynthetic reaction center / Green sulfur bacteria / Energy transfer | ||||||
Function / homology | Function and homology information thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chlorobaculum tepidum (bacteria) Chlorobaculum tepidum TLS (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Chen, J.H. / Zhang, X. | ||||||
Citation | Journal: Science / Year: 2020 Title: Architecture of the photosynthetic complex from a green sulfur bacterium. Authors: Jing-Hua Chen / Hangjun Wu / Caihuang Xu / Xiao-Chi Liu / Zihui Huang / Shenghai Chang / Wenda Wang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Abstract: The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo- ...The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6m32.cif.gz | 514.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m32.ent.gz | 456.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m32_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 6m32_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6m32_validation.xml.gz | 106.5 KB | Display | |
Data in CIF | 6m32_validation.cif.gz | 136.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/6m32 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/6m32 | HTTPS FTP |
-Related structure data
Related structure data | 30069MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem P840 reaction ... , 2 types, 3 molecules BAa
#3: Protein | Mass: 23540.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KAY1 |
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#4: Protein | Mass: 81784.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / References: UniProt: Q8KAY0 |
-Bacteriochlorophyll ... / Protein , 2 types, 4 molecules EFGD
#1: Protein | Mass: 40343.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q46393 #2: Protein | | Mass: 16633.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KEP5 |
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-Non-polymers , 9 types, 67 molecules
#5: Chemical | ChemComp-BCL / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | ChemComp-G2O / |
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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 |
-Sample preparation
Component | Name: FMO-RC of green sulfur bacteria / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38244 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 9156 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 4 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3947008 / Details: raw particles | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268430 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.23 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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