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- PDB-1bgy: CYTOCHROME BC1 COMPLEX FROM BOVINE -

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Basic information

Entry
Database: PDB / ID: 1bgy
TitleCYTOCHROME BC1 COMPLEX FROM BOVINE
Components(CYTOCHROME BC1 ...) x 11
KeywordsELECTRON TRANSPORT / CYTOCHROME / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / 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 / pyramidal neuron development / Respiratory electron transport / 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 / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome b-c1 complex subunit 10 ...Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / 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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / 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 ...FE2/S2 (INORGANIC) CLUSTER / HEME C / 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 / molecular replacement / Resolution: 3 Å
AuthorsIwata, S. / Lee, J.W. / Okada, K. / Lee, J.K. / Iwata, M. / Ramaswamy, S. / Jap, B.K.
CitationJournal: Science / Year: 1998
Title: Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.
Authors: Iwata, S. / Lee, J.W. / Okada, K. / Lee, J.K. / Iwata, M. / Rasmussen, B. / Link, T.A. / Ramaswamy, S. / Jap, B.K.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME BC1 COMPLEX
B: CYTOCHROME BC1 COMPLEX
C: CYTOCHROME BC1 COMPLEX
D: CYTOCHROME BC1 COMPLEX
E: CYTOCHROME BC1 COMPLEX
F: CYTOCHROME BC1 COMPLEX
G: CYTOCHROME BC1 COMPLEX
H: CYTOCHROME BC1 COMPLEX
I: CYTOCHROME BC1 COMPLEX
J: CYTOCHROME BC1 COMPLEX
K: CYTOCHROME BC1 COMPLEX
M: CYTOCHROME BC1 COMPLEX
N: CYTOCHROME BC1 COMPLEX
O: CYTOCHROME BC1 COMPLEX
P: CYTOCHROME BC1 COMPLEX
Q: CYTOCHROME BC1 COMPLEX
R: CYTOCHROME BC1 COMPLEX
S: CYTOCHROME BC1 COMPLEX
T: CYTOCHROME BC1 COMPLEX
U: CYTOCHROME BC1 COMPLEX
V: CYTOCHROME BC1 COMPLEX
W: CYTOCHROME BC1 COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,15129
Polymers482,27222
Non-polymers3,8797
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area83890 Å2
ΔGint-581 kcal/mol
Surface area166000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.110, 130.110, 720.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.066, 0.136, 0.988), (0.136, -0.98, 0.144), (0.988, 0.144, 0.046)
Vector: 1.325, 184.252, -26.658)

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Components

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CYTOCHROME BC1 ... , 11 types, 22 molecules AMBNCODPEQFRGSHTIUJVKW

#1: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P23004, quinol-cytochrome-c reductase
#3: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00125, quinol-cytochrome-c reductase
#5: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00126, quinol-cytochrome-c reductase
#9: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7964.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 6370.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07552, quinol-cytochrome-c reductase

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Non-polymers , 3 types, 7 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 61.5 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.015 %n-dodecyl-beta-D-maltoside11
2100 mM11NaCl
38 %PEG400011
4HECAMEG11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 111672 / % possible obs: 81.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.92 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.9 / % possible all: 27.9
Reflection
*PLUS
Num. measured all: 440419
Reflection shell
*PLUS
% possible obs: 27.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1BE3

1be3


Resolution: 3→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.36 2022 2 %RANDOM
Rwork0.32 ---
obs-101111 74 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31468 0 262 0 31730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7363
X-RAY DIFFRACTIONp_mcangle_it2.683.5
X-RAY DIFFRACTIONp_scbond_it3.0334
X-RAY DIFFRACTIONp_scangle_it4.4375.5
X-RAY DIFFRACTIONp_plane_restr0.02490.03
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.2220.3
X-RAY DIFFRACTIONp_multtor_nbd0.30.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2330.3
X-RAY DIFFRACTIONp_planar_tor6.27
X-RAY DIFFRACTIONp_staggered_tor26.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.420
X-RAY DIFFRACTIONp_special_tor

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