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- PDB-7f0l: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -
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Basic information
Entry | Database: PDB / ID: 7f0l | |||||||||||||||||||||
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Title | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES MONOMER | |||||||||||||||||||||
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![]() | PHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA | |||||||||||||||||||||
Function / homology | ![]() organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||||||||||||||
![]() | Tani, K. / Nagashima, V.P. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Ji, X.-C. / Hall, M. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. ...Tani, K. / Nagashima, V.P. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Ji, X.-C. / Hall, M. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Wang-Otomo, Z.-Y. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex. Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / ...Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo / ![]() ![]() ![]() Abstract: Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is ...Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general. | |||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 501.8 KB | Display | ![]() |
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PDB format | ![]() | 457.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 4.8 MB | Display | ![]() |
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Full document | ![]() | 5.1 MB | Display | |
Data in XML | ![]() | 117.7 KB | Display | |
Data in CIF | ![]() | 145.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31400MC 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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Components
-Protein , 3 types, 3 molecules LXU
#1: Protein | Mass: 31491.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 9017.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 5555.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Reaction center protein ... , 2 types, 2 molecules MH
#2: Protein | Mass: 34543.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 28091.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: WP_069330428.1 / Source: (natural) ![]() |
-Light-harvesting protein B-875 alpha ... , 2 types, 14 molecules ADFIKOQSVY1357
#4: Protein | Mass: 6473.780 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: WP_069330428.1 / Source: (natural) ![]() #6: Protein | Mass: 6445.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein/peptide / Sugars , 2 types, 38 molecules BEGJNPRTWZ2468![](data/chem/img/LMT.gif)
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#16: Sugar | ChemComp-LMT / #5: Protein/peptide | Mass: 5592.361 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 8 types, 88 molecules ![](data/chem/img/BCL.gif)
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![](data/chem/img/LDA.gif)
![](data/chem/img/FE.gif)
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![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/PGV.gif)
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#9: Chemical | ChemComp-BCL / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-PGV / ( #13: Chemical | ChemComp-LDA / #14: Chemical | ChemComp-FE / | #15: Chemical | ChemComp-SPO / #17: Chemical | ChemComp-CDL / |
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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: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides monomer Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: ![]() Strain: IL106 |
Buffer solution | pH: 8 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. |
Specimen support | Grid material: MOLYBDENUM |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.275 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 551846 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160448 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 60 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5Y5S | ||||||||||||||||||||||||||||||||
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