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Yorodumi- PDB-7vy2: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -
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-Basic information
Entry | Database: PDB / ID: 7vy2 | |||||||||||||||||||||
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Title | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER | |||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA | |||||||||||||||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / 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 | Rhodobacter sphaeroides f. sp. denitrificans (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||||||||||||||
Authors | Tani, K. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Nagashima, K.V.P. / Hall, M. / Takahashi, A. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. ...Tani, K. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Nagashima, K.V.P. / Hall, M. / Takahashi, A. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Wang-Otomo, Z.-Y. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: Nat Commun / Year: 2022 Title: Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex. Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / ...Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo / Abstract: Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM ...Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vy2.cif.gz | 983.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vy2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7vy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/7vy2 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/7vy2 | HTTPS FTP |
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-Related structure data
Related structure data | 32192MC 7vy3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosynthetic reaction center ... , 2 types, 4 molecules LlHh
#1: Protein | Mass: 31360.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QV46 #3: Protein | Mass: 28091.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QV87 |
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-Protein , 3 types, 6 molecules MmXxUu
#2: Protein | Mass: 34412.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QV86 #6: Protein | Mass: 8886.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QV32 #7: Protein | Mass: 5555.558 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QU05 |
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-Antenna pigment protein ... , 2 types, 56 molecules ADFIKOQSVY1357adfikoqsvy01030507BE...
#4: Protein | Mass: 6473.780 Da / Num. of mol.: 28 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6W8S0 #5: Protein/peptide | Mass: 5461.166 Da / Num. of mol.: 28 / Source method: isolated from a natural source Source: (natural) Rhodobacter sphaeroides f. sp. denitrificans (bacteria) References: UniProt: A0A7Z6QV72 |
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-Sugars , 1 types, 27 molecules
#11: Sugar | ChemComp-LMT / |
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-Non-polymers , 9 types, 174 molecules
#8: Chemical | ChemComp-BCL / #9: Chemical | ChemComp-BPH / #10: Chemical | ChemComp-U10 / #12: Chemical | ChemComp-PGV / ( #13: Chemical | #14: Chemical | ChemComp-SPO / #15: Chemical | ChemComp-CDL / #16: Chemical | ChemComp-PTY / #17: Chemical | ChemComp-LDA / | |
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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 |
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Molecular weight |
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Source (natural) |
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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. | ||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K |
-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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / 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) |
-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: 164496 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124916 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 60 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7F0L | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.43 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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