+Open data
-Basic information
Entry | Database: PDB / ID: 3l74 | |||||||||
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Title | Cytochrome BC1 complex from chicken with famoxadone bound | |||||||||
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 PROTEIN / UBIQUINONE / AZOXYSTROBIN OXIDOREDUCTASE / REDOX ENZYME RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE / MEMBRANE / STROBILURINS BINDING / MITOCHONDRION / TRANSMEMBRANE / STIGMATELLIN / IRON / MITOCHONDRIAL INNER MEMBRANE / RESPIRATORY CHAIN / IRON-SULFUR / TRANSIT PEPTIDE / Metal-binding / Mitochondrion inner membrane / Transport / Disulfide bond | |||||||||
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 / RIGID BODY REFINEMENT / Resolution: 2.76 Å | |||||||||
Authors | Huang, L. / Berry, E.A. | |||||||||
Citation | Journal: To be Published Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen ...Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors. Authors: Huang, L. / 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 | 3l74.cif.gz | 827.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l74.ent.gz | 661.4 KB | Display | PDB format |
PDBx/mmJSON format | 3l74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/3l74 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l74 | HTTPS FTP |
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-Related structure data
Related structure data | 3l71C 3l72C 3l73C 3h1hS C: citing same article (ref.) 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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-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, 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: UniProt: D0VX29, 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, quinol-cytochrome-c reductase |
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-CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 2 types, 4 molecules ERIV
#5: Protein | Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: UNP 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: UNP RESIDUES 45-76 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase |
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-MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 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: UniProt: D0VX30, 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, 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: UniProt: D0VX28, 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, quinol-cytochrome-c reductase |
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-Sugars , 1 types, 6 molecules
#17: Sugar | ChemComp-BOG / |
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-Non-polymers , 10 types, 63 molecules
#11: Chemical | ChemComp-PEE / #12: Chemical | ChemComp-UNL / Num. of mol.: 11 / Source method: obtained synthetically #13: Chemical | ChemComp-HEM / #14: Chemical | #15: Chemical | #16: Chemical | #18: Chemical | #19: Chemical | ChemComp-CDL / #20: Chemical | #21: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE COMPLETE SEQUENCE OF CHAIN I AND V IS ...THE COMPLETE SEQUENCE OF CHAIN I AND V IS MLSVAARSGP |
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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: 4.07 Å3/Da / Density % sol: 69.76 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.77 Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH ...Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH 6.77 , VAPOR DIFFUSION, SITTING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2006 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→99 Å / Num. all: 201091 / Num. obs: 201091 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 71.9 Å2 / Rsym value: 0.078 / Net I/σ(I): 17.8 | |||||||||
Reflection shell | Resolution: 2.7→2.74 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.891 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: PDB ENTRY 3H1H Resolution: 2.76→58.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3668486.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.8445 Å2 / ksol: 0.289886 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.76→58.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.76→2.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 7
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Xplor file |
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