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Yorodumi- PDB-8wdv: Photosynthetic LH1-RC complex from the purple sulfur bacterium Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wdv | |||||||||||||||||||||
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Title | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by Ca2+-DEAE | |||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE SULFUR 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 / electron transfer activity / iron ion binding / heme binding ...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 / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Allochromatium vinosum DSM 180 (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å | |||||||||||||||||||||
Authors | Tani, K. / Kanno, R. / Harada, A. / Kobayashi, A. / Minamino, A. / Nakamura, N. / Ji, X.-C. / Purba, E.R. / Hall, M. / Yu, L.-J. ...Tani, K. / Kanno, R. / Harada, A. / Kobayashi, A. / Minamino, A. / Nakamura, N. / Ji, X.-C. / Purba, E.R. / Hall, M. / Yu, L.-J. / Madigan, M.T. / Mizoguchi, A. / Iwasaki, K. / Humbel, B.M. / Kimura, Y. / Wang-Otomo, Z.-Y. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: Commun Biol / Year: 2024 Title: High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum Authors: Tani, K. / Kanno, R. / Harada, A. / Kobayashi, Y. / Minamino, A. / Takenaka, S. / Nakamura, N. / Ji, X.C. / Purba, E.R. / Hall, M. / Yu, L.J. / Madigan, M.T. / Mizoguchi, A. / Iwasaki, K. / ...Authors: Tani, K. / Kanno, R. / Harada, A. / Kobayashi, Y. / Minamino, A. / Takenaka, S. / Nakamura, N. / Ji, X.C. / Purba, E.R. / Hall, M. / Yu, L.J. / Madigan, M.T. / Mizoguchi, A. / Iwasaki, K. / Humbel, B.M. / Kimura, Y. / Wang-Otomo, Z.Y. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wdv.cif.gz | 662.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wdv.ent.gz | 559.3 KB | Display | PDB format |
PDBx/mmJSON format | 8wdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/8wdv ftp://data.pdbj.org/pub/pdb/validation_reports/wd/8wdv | HTTPS FTP |
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-Related structure data
Related structure data | 37466MC 8wduC 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, 2 molecules CH
#1: Protein | Mass: 41512.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: O82947 |
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#4: Protein | Mass: 28231.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RPF6 |
-Reaction center protein ... , 2 types, 2 molecules LM
#2: Protein | Mass: 31217.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: P51762 |
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#3: Protein | Mass: 36364.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: P51763 |
-Antenna complex alpha/beta ... , 5 types, 32 molecules AIKOQ1579BJNPR24680DFSUWYEGTVXZ3
#5: Protein/peptide | Mass: 5136.131 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP69 #6: Protein/peptide | Mass: 5269.103 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP75 #7: Protein | Mass: 7244.583 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP74 #8: Protein/peptide | Mass: 5518.472 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP68 #9: Protein | | Mass: 7392.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP67 |
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-Sugars , 1 types, 19 molecules
#24: Sugar | ChemComp-LMT / |
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-Non-polymers , 15 types, 446 molecules
#10: Chemical | ChemComp-HEM / #11: Chemical | ChemComp-MG / | #12: Chemical | ChemComp-CA / #13: Chemical | ChemComp-Z41 / ( | #14: Chemical | ChemComp-PLM / | #15: Chemical | ChemComp-PGV / ( #16: Chemical | ChemComp-BCL / #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-FE / | #20: Chemical | ChemComp-MQ8 / | #21: Chemical | ChemComp-CRT / #22: Chemical | ChemComp-CDL / #23: Chemical | #25: Water | ChemComp-HOH / | |
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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 | Name: Photosynthetic LH1-RC complex from the purple sulfur phototrophic bacterium Allochromatium vinosum Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Allochromatium vinosum DSM 180 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5.2 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: 90 % / 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: 2600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 30.15 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 833998 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219233 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 63 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7VRJ Accession code: 7VRJ / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
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