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- PDB-1qcr: CRYSTAL STRUCTURE OF BOVINE MITOCHONDRIAL CYTOCHROME BC1 COMPLEX,... -

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Basic information

Entry
Database: PDB / ID: 1qcr
TitleCRYSTAL STRUCTURE OF BOVINE MITOCHONDRIAL CYTOCHROME BC1 COMPLEX, ALPHA CARBON ATOMS ONLY
Components(UBIQUINOL CYTOCHROME C ...) x 11
KeywordsOXIDOREDUCTASE / BC1 / QCR / MEMBRANE PROTEIN / PROTON TRANSLOCATION / ELECTRON TRANSFER / PROTEASE / MPP / MITOCHONDRIAL PROCESSING PEPTIDASE / CYTOCHROME C1 / CYTOCHROME B / RIESKE / IRON SULFER PROTEIN
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / Respiratory electron transport / pyramidal neuron development / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / Respiratory electron transport / pyramidal neuron development / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / metalloendopeptidase activity / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsXia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A. / Zhang, L. / Yu, L. / Deisenhofer, J.
Citation
Journal: Science / Year: 1997
Title: Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.
Authors: Xia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A.M. / Zhang, L. / Yu, L. / Deisenhofer, J.
#1: Journal: Science / Year: 1997
Title: Erratum. Crystal Structure of the Cytochrome Bc1 Complex from Bovine Heart Mitochondria
Authors: Xia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A.M. / Zhang, L. / Yu, L. / Deisenhofer, J.
History
DepositionMay 17, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
B: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
C: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
D: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
E: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
F: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
G: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
H: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
I: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
J: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
K: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,71312
Polymers210,09611
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.500, 153.500, 597.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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UBIQUINOL CYTOCHROME C ... , 11 types, 11 molecules ABCDEFGHIJK

#1: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 49252.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 45023.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P23004, quinol-cytochrome-c reductase
#3: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 42489.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 8785.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00125, quinol-cytochrome-c reductase
#5: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 12731.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 8287.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 7090.942 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00126, quinol-cytochrome-c reductase
#9: Protein/peptide UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 2806.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 6927.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein/peptide UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 / QCR / Coordinate model: Cα atoms only


Mass: 5060.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P07552, quinol-cytochrome-c reductase

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Non-polymers , 1 types, 1 molecules

#12: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 100

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlcomplex11
250 mMMOPS11
320 mMammonium acetate11
420 %glycerol11
50.1 %DMG11can be replaced by 0.1% SPC
612 %PEG400012
750 mMMOPS12
80.5 M12KCl
920 %glycerol12
100.1 %detergent12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.55
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 72196 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1 / % possible all: 62.4
Reflection
*PLUS
Num. measured all: 2166501
Reflection shell
*PLUS
% possible obs: 62.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→10 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.375 --
Rwork0.3 --
obs0.3 72196 90.6 %
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 43 0 1926
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.3 / Rfactor Rwork: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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