+Open data
-Basic information
Entry | Database: PDB / ID: 3h1h | ||||||
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Title | Cytochrome bc1 complex from chicken | ||||||
Components |
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Keywords | OXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEASE / UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / Electron transport / Heme / Iron / Membrane / Metal-binding / Mitochondrion / Mitochondrion inner membrane / Transmembrane / Transport / Disulfide bond / Iron-sulfur / Transit peptide | ||||||
Function / homology | Function and homology information Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane ...Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / heme binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.16 Å | ||||||
Authors | Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Electron Transfer by Domain Movement in Cytochrome Bc1 Authors: Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H. #1: Journal: J.Mol.Biol. / Year: 2005 Title: Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial Bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-Bonding Pattern. Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A. #2: Journal: J.BIOENERG.BIOMEMBR. / Year: 1999 Title: The Structure of the Avian Mitochondrial Cytochrome bc1 Complex. Authors: Berry, E.A. / Huang, L.S. / Zhang, Z. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h1h.cif.gz | 813.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h1h.ent.gz | 660.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1h ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1h | HTTPS FTP |
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-Related structure data
Related structure data | 1bccC 2bccC 3bccC 3h1iC 3h1jC 2ppj C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO
#1: Protein | Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) References: UniProt: D0VX31*PLUS, quinol-cytochrome-c reductase #2: Protein | Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: quinol-cytochrome-c reductase |
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-Protein , 2 types, 4 molecules CPDQ
#3: Protein | Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946, quinol-cytochrome-c reductase #4: Protein | Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) References: UniProt: D0VX26*PLUS, quinol-cytochrome-c reductase |
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-Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules ERIV
#5: Protein | Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: sequence database residues 77-272 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase #9: Protein/peptide | Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-76 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase |
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-UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ... , 4 types, 8 molecules FSGTHUJW
#6: Protein | Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: quinol-cytochrome-c reductase #7: Protein | Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) References: UniProt: D0VX32*PLUS, quinol-cytochrome-c reductase #8: Protein | Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: quinol-cytochrome-c reductase #10: Protein | Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) References: UniProt: D0VX27*PLUS, quinol-cytochrome-c reductase |
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-Sugars , 1 types, 5 molecules
#18: Sugar | ChemComp-BOG / |
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-Non-polymers , 9 types, 50 molecules
#11: Chemical | ChemComp-UNL / Num. of mol.: 9 / Source method: obtained synthetically #12: Chemical | ChemComp-HEM / #13: Chemical | #14: Chemical | ChemComp-CDL / #15: Chemical | ChemComp-PEE / #16: Chemical | #17: Chemical | #19: Chemical | #20: Water | ChemComp-HOH / | |
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-Details
Sequence details | IN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ...IN THE COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1995 / Details: CYL.-BENT MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→69.338 Å / Num. all: 123869 / Num. obs: 123869 / % possible obs: 91.6 % / Observed criterion σ(I): -2 / Redundancy: 4.5 % / Biso Wilson estimate: 79.4 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.102 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.16→3.27 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.4 / % possible all: 84.5 |
-Processing
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Refinement | Method to determine structure: MIR / Resolution: 3.16→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4383576.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Heavy Atoms in derivatives of chicken bc1 crystals were located using XtalView, then refined and used for phase calculation in ccp4 mlphare. Nonisomorphous crystals of beef, rabbit bc1 were ...Details: Heavy Atoms in derivatives of chicken bc1 crystals were located using XtalView, then refined and used for phase calculation in ccp4 mlphare. Nonisomorphous crystals of beef, rabbit bc1 were solved by molecular replacement using cut-out density. The phases were improved by cross-crystal and NCS density averaging using RAVE from USF. Model building was carried out in the best native chicken crystal, resulting in structure 1bcc. This structure is a further refinement against the original data, with correct sequences for the subunits and with minor errors in the orifginal tracing corrected.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.7533 Å2 / ksol: 0.271593 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.16→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.16→3.33 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 7
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Xplor file |
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