[English] 日本語
Yorodumi- PDB-8gwa: Structure of the intact photosynthetic light-harvesting antenna-r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gwa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium | |||||||||
Components |
| |||||||||
Keywords | PHOTOSYNTHESIS / Green sulfur bacterium / Reaction center / FMO protein / Energy transfer | |||||||||
Function / homology | Function and homology information thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Chlorobaculum tepidum TLS (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Chen, J.H. / Zhang, X. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: J Integr Plant Biol / Year: 2023 Title: Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium. Authors: Jing-Hua Chen / Weiwei Wang / Chen Wang / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Abstract: The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson ...The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gwa.cif.gz | 805.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gwa.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8gwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gwa_validation.pdf.gz | 5.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gwa_full_validation.pdf.gz | 6.1 MB | Display | |
Data in XML | 8gwa_validation.xml.gz | 177.3 KB | Display | |
Data in CIF | 8gwa_validation.cif.gz | 226.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/8gwa ftp://data.pdbj.org/pub/pdb/validation_reports/gw/8gwa | HTTPS FTP |
-Related structure data
Related structure data | 34307MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Bacteriochlorophyll ... , 1 types, 6 molecules 132465
#1: Protein | Mass: 40343.430 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q46393 |
---|
-Protein , 4 types, 5 molecules DEFCc
#2: Protein | Mass: 16633.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KEP5 |
---|---|
#5: Protein | Mass: 4954.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) |
#6: Protein | Mass: 6227.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KG87 |
#7: Protein | Mass: 22741.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: O07091 |
-Photosystem P840 reaction ... , 2 types, 3 molecules BAa
#3: Protein | Mass: 23383.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KAY1 |
---|---|
#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 |
-Non-polymers , 10 types, 103 molecules
#8: Chemical | ChemComp-BCL / #9: Chemical | ChemComp-CDL / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-G2O / #13: Chemical | ChemComp-F39 / [( #14: Chemical | ChemComp-LHG / #15: Chemical | #16: Chemical | #17: Chemical | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GsbRC-2FMO complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlorobaculum tepidum TLS (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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: 130000 X / Calibrated magnification: 152200 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 80 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2297 |
EM imaging optics | Energyfilter name: TFS Selectris / Chromatic aberration corrector: 2.7mm / Energyfilter slit width: 10 eV / Spherical aberration corrector: 2.7mm |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1961370 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227038 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refine LS restraints |
|