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Yorodumi- PDB-3cwb: Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cwb | |||||||||
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Title | Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / Crocacin D / inhibitor design / structure-activity relationship / polyketide / fungicide / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEA UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / Electron transport / Heme / Inner membrane / Iron / Membrane / Metal-binding / Mitochondrion / Transmembrane / Transport | |||||||||
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 / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity ...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 / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 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 / Rigid Body Refinement / Resolution: 3.51 Å | |||||||||
Authors | Huang, L. / Cromartie, T. / Viner, R. / Crowley, P.J. / Berry, E.A. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Authors: Crowley, P.J. / Berry, E.A. / Cromartie, T. / Daldal, F. / Godfrey, C.R. / Lee, D.W. / Phillips, J.E. / Taylor, A. / Viner, R. #1: 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. #2: Journal: J.Mol.Biol. / Year: 2005 Title: Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern. Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cwb.cif.gz | 833.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cwb.ent.gz | 665.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/3cwb ftp://data.pdbj.org/pub/pdb/validation_reports/cw/3cwb | HTTPS FTP |
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-Related structure data
Related structure data | 1bccS S: Starting model for refinement |
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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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Details | The biological unit is a homodimer of hetero-11-mers. Subunit 11 is not essential for activity and is missing in our preparation. The asymmetric unit of this crystal form contains one copy of the biological unit, two copies each of 10 proteins. The deposited structure is the asymmetric unit. |
-Components
-MITOCHONDRIAL 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 #2: Protein | Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX29*PLUS |
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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 #4: Protein | Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) |
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-MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 6 types, 12 molecules ERFSGTHUIVJW
#5: Protein | Mass: 21506.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5*PLUS #6: Protein | Mass: 13394.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX30*PLUS #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 #8: Protein | Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX28*PLUS #9: Protein | Mass: 5211.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5 #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 |
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-Sugars , 1 types, 6 molecules
#12: Sugar | ChemComp-BOG / |
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-Non-polymers , 10 types, 44 molecules
#11: Chemical | ChemComp-PEE / #13: Chemical | #14: Chemical | ChemComp-HEM / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-CDL / #19: Chemical | #20: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #21: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 1-446 OF ENTITY 1 = 33-478 OF NCBI XM_414356.2; RESIDUES 1-441 OF ENTITY 2 = 17-457 OF ...RESIDUES 1-446 OF ENTITY 1 = 33-478 OF NCBI XM_414356.2; RESIDUES 1-441 OF ENTITY 2 = 17-457 OF NCBI XM_424611.2; RESIDUES 1-380 OF ENTITY 3 = 1-380 OF NCBI NC_001323.1; RESIDUES 1-196 OF ENTITY 5 = 77-272 OF NCBI NM_001005843.1; RESIDUES 1-110 OF ENTITY 6 = 2-111 OF NCBI XM_418347.2; RESIDUES 1-81 OF ENTITY 7 = 37-117 OF NCBI XM_414651.1; RESIDUES 1-77 OF ENTITY 8 = 2-78 OF NCBI XM_001235147.1; RESIDUES 1-76 OF ENTITY 9 = 1-76 OF NCBI NM_001005843.1 (NOTE THIS IS THE SAME GENE AS ENTITY 5); RESIDUES 1-56 OF ENTITY 10 = 8-63 OF NCBI XM_001234249.1. FOR ENTITY 4 , THERE IS NO ANNOTATED ORF COVERING THE SEQUENCE, BUT THE NUCLEOTIDE |
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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: 4.19 Å3/Da / Density % sol: 70.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 20MM KMES, 75MM NACL, 10% GLYCEROL, 6% PEG4000. Crystal soaked with the inhibitor and RbBr salt, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.741439, 1.239798, 0.920205 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.5→60 Å / Num. obs: 96135 / % possible obs: 92.1 % / Observed criterion σ(I): -2 / Redundancy: 2.9 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.178 / Net I/σ(I): 5 | ||||||||||||
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.99 / % possible all: 78.9 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Refinement Starting model: PDB ENTRY 1BCC AFTER FURTHER REFINEMENT Resolution: 3.51→21.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7037765.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Three datasets were obtained at different wavelengths. Data reduction statistics are given for the second wavelength, 1.239798 A, except for R-merge which is from merging the three datasets. ...Details: Three datasets were obtained at different wavelengths. Data reduction statistics are given for the second wavelength, 1.239798 A, except for R-merge which is from merging the three datasets. Refinement was against the resulting single merged dataset. The purpose of the multiple wavelength data collection was to locate the iodine atom in the inhibitor (successful) and cation and anion (RbCl) binding sites (unsuccesful). Only the merged data is deposited. Entity 9 is mobile in the crystals, occupying two or more different position. Only the major position is modeled. Overall occupancy was refined for this domain resulting in occupancy less than 1.0 for chain E in its predominant position. Some of the lipid and detergent molecules also refined to occupancy less than 1.0.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 12.8267 Å2 / ksol: 0.22 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.51→21.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.51→3.58 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 15
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