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

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Entry
Database: PDB / ID: 1bgy
TitleCYTOCHROME BC1 COMPLEX FROM BOVINE
Components(CYTOCHROME BC1 ...Coenzyme Q – cytochrome c reductase) x 11
KeywordsELECTRON TRANSPORT / CYTOCHROME / MEMBRANE PROTEIN
Function / homologyDi-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Rieske iron-sulphur protein, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, C-terminal / Cytochrome b-c1 complex subunit 9 / Cytochrome c-like domain / Globular protein, non-globular alpha/beta subunit / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, N-terminal ...Di-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Rieske iron-sulphur protein, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, C-terminal / Cytochrome b-c1 complex subunit 9 / Cytochrome c-like domain / Globular protein, non-globular alpha/beta subunit / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, N-terminal / Rieske iron-sulphur protein / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Rieske [2Fe-2S] domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome b/b6, N-terminal / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b/b6-like domain superfamily / Single alpha-helix domain superfamily / Cytochrome b / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome c-like domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b/b6, C-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome b/b6/petB / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Respiratory electron transport / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c family profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6 N-terminal region profile. / Insulinase family, zinc-binding region signature. / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Peptidase M16 inactive domain / Cytochrome b(C-terminal)/b6/petD / UcrQ family / Cytochrome C1 family / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome c1 / Peptidase M16, zinc-binding site / Insulinase (Peptidase family M16) / Ubiquinol-cytochrome C reductase hinge protein / Ubiquinol-cytochrome C reductase complex 14kD subunit / Ubiquinol cytochrome reductase transmembrane region / intrinsic component of mitochondrial membrane / mitochondrial respiratory chain complex III assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / integral component of mitochondrial membrane / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial ATP synthesis coupled proton transport / mitochondrial respiratory chain complex IV / ubiquinone binding / respiratory electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / aerobic respiration / 2 iron, 2 sulfur cluster binding / catalytic activity / metalloendopeptidase activity / mitochondrial inner membrane / oxidation-reduction process / heme binding / mitochondrion / integral component of membrane / metal ion binding / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 7 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / 3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 2, 1998 / Release: Jan 6, 1999
RevisionDateData content typeGroupProviderType
1.0Jan 6, 1999Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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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
Polyers482,27222
Non-polymers3,8797
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)83890
ΔGint (kcal/M)-581
Surface area (Å2)166000
MethodPISA
Unit cell
γ
α
β
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-MP 65

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Components

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

#1: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 49266.254 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 46575.469 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P23004, quinol-cytochrome-c reductase
#3: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 42620.340 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 27323.277 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00125, quinol-cytochrome-c reductase
#5: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 21640.580 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 13371.190 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9606.027 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9189.116 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00126, quinol-cytochrome-c reductase
#9: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7964.259 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7209.311 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein/peptide CYTOCHROME BC1 COMPLEX / Coenzyme Q – cytochrome c reductase / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 6370.390 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / Genus: Bos
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial 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 / Formula: C34H32FeN4O4 / Heme
#13: Chemical ChemComp-HEC / HEME C


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


Mass: 175.820 Da / Num. of mol.: 1 / Formula: Fe2S2

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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 / Density percent sol: 61.5 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Aug 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 29.4 Å2 / D resolution high: 3 Å / D resolution low: 4 Å / Number obs: 111672 / Rmerge I obs: 0.92 / NetI over sigmaI: 8.9 / Redundancy: 3.9 % / Percent possible obs: 81.9
Reflection shellRmerge I obs: 0.24 / Highest resolution: 3 Å / Lowest resolution: 3.11 Å / MeanI over sigI obs: 1.9 / Percent possible all: 27.9
Reflection
*PLUS
Number measured all: 440419
Reflection shell
*PLUS
Percent possible obs: 27.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefineMethod to determine structure: molecular replacement
Starting model: 1BE3
R Free selection details: RANDOM / Cross valid method: THROUGHOUT
Displacement parametersB iso mean: 3 Å2
Least-squares processR factor R free: 0.36 / R factor R work: 0.32 / Highest resolution: 3 Å / Lowest resolution: 2 Å / Number reflection R free: 2022 / Number reflection obs: 101111 / Percent reflection R free: 2 / Percent reflection obs: 74
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 31468 / Nucleic acid: 0 / Ligand: 262 / Solvent: 0 / Total: 31730
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0100.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0500.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7363.00
X-RAY DIFFRACTIONp_mcangle_it2.6803.50
X-RAY DIFFRACTIONp_scbond_it3.0334.00
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_nbd0.2220.30
X-RAY DIFFRACTIONp_multtor_nbd0.3000.30
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2330.30
X-RAY DIFFRACTIONp_planar_tor6.27.0
X-RAY DIFFRACTIONp_staggered_tor26.715.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.420.00
X-RAY DIFFRACTIONp_special_tor

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