+Open data
-Basic information
Entry | Database: PDB / ID: 7uea | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Photosynthetic assembly of Chlorobaculum tepidum (RC-FMO1) | |||||||||
Components |
| |||||||||
Keywords | PHOTOSYNTHESIS / FMO / reaction center / single-particle cryo-EM / bacteriochlorophyll / electron transport chain / 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: 3.49 Å | |||||||||
Authors | Puskar, R. / Truong, C.D. / Swain, K. / Li, S. / Cheng, K.-W. / Wang, T.Y. / Poh, Y.-P. / Liu, H. / Chou, T.-F. / Nannenga, B. / Chiu, P.-L. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria. Authors: Ryan Puskar / Chloe Du Truong / Kyle Swain / Saborni Chowdhury / Ka-Yi Chan / Shan Li / Kai-Wen Cheng / Ting Yu Wang / Yu-Ping Poh / Yuval Mazor / Haijun Liu / Tsui-Fen Chou / Brent L Nannenga / Po-Lin Chiu / Abstract: The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex ...The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7uea.cif.gz | 654.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7uea.ent.gz | 555.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uea_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7uea_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 7uea_validation.xml.gz | 117.4 KB | Display | |
Data in CIF | 7uea_validation.cif.gz | 155.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/7uea ftp://data.pdbj.org/pub/pdb/validation_reports/ue/7uea | HTTPS FTP |
-Related structure data
Related structure data | 26469MC 7uebC 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
-Photosystem P840 reaction ... , 2 types, 3 molecules AaB
#1: Protein | Mass: 81784.641 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: Q8KAY0 #2: Protein | | Mass: 23540.289 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 |
---|
-Protein , 2 types, 3 molecules CcD
#3: 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 #4: 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 |
---|
-Bacteriochlorophyll ... , 1 types, 3 molecules UVW
#5: Protein | Mass: 40343.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q46393 |
---|
-Non-polymers , 9 types, 77 molecules
#6: Chemical | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-LHG / #11: Chemical | ChemComp-LMG / #12: Chemical | #13: Chemical | ChemComp-G2O / #14: 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: Photosynthetic assembly (RC-FMO1) / Type: COMPLEX Details: Photosynthetic assembly from Chlorobaculum tepidum (RC-FMO1) Entity ID: #1-#5 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.370 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Chlorobaculum tepidum TLS (bacteria) / Cellular location: Membrane | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-2/1 | ||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-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 / Calibrated magnification: 47259 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 45.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 32898 |
Image scans | Sampling size: 5 µm / Movie frames/image: 30 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1938908 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142020 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 72.89 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6M32 Accession code: 6M32 / Source name: PDB / Type: experimental model |