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- PDB-8b64: Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from... -
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Basic information
Entry | Database: PDB / ID: 8b64 | ||||||
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Title | Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus | ||||||
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![]() | PHOTOSYNTHESIS / PufX / core complex / RC-LH1 / Rba capsulatus / photosynthetic core | ||||||
Function / homology | ![]() 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 / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.589 Å | ||||||
![]() | Bracun, L. / Yamagata, A. / Shirouzu, M. / Liu, L.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of a monomeric RC-LH1-PufX supercomplex with high-carotenoid content from Rhodobacter capsulatus. Authors: Laura Bracun / Atsushi Yamagata / Bern M Christianson / Mikako Shirouzu / Lu-Ning Liu / ![]() ![]() ![]() Abstract: In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial ...In purple photosynthetic bacteria, the photochemical reaction center (RC) and light-harvesting complex 1 (LH1) assemble to form monomeric or dimeric RC-LH1 membrane complexes, essential for bacterial photosynthesis. Here, we report a 2.59-Å resolution cryoelectron microscopy (cryo-EM) structure of the RC-LH1 supercomplex from Rhodobacter capsulatus. We show that Rba. capsulatus RC-LH1 complexes are exclusively monomers in which the RC is surrounded by a 15-subunit LH1 ring. Incorporation of a transmembrane polypeptide PufX leads to a large opening within the LH1 ring. Each LH1 subunit associates two carotenoids and two bacteriochlorophylls, which is similar to Rba. sphaeroides RC-LH1 but more than one carotenoid per LH1 in Rba. veldkampii RC-LH1 monomer. Collectively, the unique Rba. capsulatus RC-LH1-PufX represents an intermediate structure between Rba. sphaeroides and Rba. veldkampii RC-LH1-PufX. Comparison of PufX from the three Rhodobacter species indicates the important residues involved in dimerization of RC-LH1. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 613 KB | Display | ![]() |
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PDB format | ![]() | 454.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 114 KB | Display | |
Data in CIF | ![]() | 143.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15862MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 16 molecules aebdtsuronkjigfX
#1: Protein | Mass: 6600.920 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 8574.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein/peptide , 1 types, 15 molecules DAEBSTUORKNIJFG
#2: Protein/peptide | Mass: 5470.303 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Reaction center protein ... , 3 types, 3 molecules LMH
#4: Protein | Mass: 31586.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 34462.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 28569.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 75 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/FE.gif)
#7: Chemical | ChemComp-BCL / #8: Chemical | ChemComp-SPO / #9: Chemical | #10: Chemical | ChemComp-U10 / #11: Chemical | ChemComp-3PE / #12: Chemical | ChemComp-FE / | |
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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-LH1-PufX photosynthetic core complex from Rba. capsulatus Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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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 defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50.32 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.589 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181054 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.23 Å2 | ||||||||||||||||||||||||
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