2YBB

Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

Structural Biology Knowledgebase: 2YBB SBKB.org


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.0 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice
  • Reconstruction Method: Single Particle

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YBB

Classification: OXIDOREDUCTASE

Total Structure Weight: 1125234.50

Macromolecule Entities
Molecule Chains Length Organism Details
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1 1 438 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO1 (51KDA)
Gene Name(s): nqo1 TTHA0089
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2 2 181 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO2 (24KDA)
Gene Name(s): nqo2 TTHA0088
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 3 3 783 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO3 (75KDA)
Gene Name(s): nqo3 TTHA0090
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4 4 409 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO4 (49KDA)
Gene Name(s): nqo4 TTHA0087
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5 5 207 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO5 (30KDA)
Gene Name(s): nqo5 TTHA0086
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6 6 181 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO6 (PSST)
Gene Name(s): nqo6 TTHA0085
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15 7 129 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO15
Gene Name(s): nqo15 TTHA0496
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9 8 182 Thermus thermophilus EC#: 1.6.5.11 IUBMB
Details: NQO9 (TYKY)
Gene Name(s): nqo9 TTHA0092
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL A, a 446 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRC1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL B, b 439 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRC2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B C, c 379 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): MT-CYB Gene View COB CYTB MTCYB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL D, d 241 Bos taurus EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 85-325
Gene Name(s): CYC1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL E, e 196 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRFS1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 7 F, f 110 Bos taurus EC#: 1.10.2.2 IUBMB
Mutation: N56D
Gene Name(s): UQCRB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 8 G, g 81 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRQ Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL H, h 78 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRH Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL I, i 65 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRFS1 Gene View
CYTOCHROME B-C1 COMPLEX SUBUNIT 9 J, j 62 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCR10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B-C1 COMPLEX SUBUNIT 10 K, k 56 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCR11 Gene View UQCR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 1 L 514 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): MT-CO1 Gene View COI COXI MTCO1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 2 M 227 Bos taurus EC#: 3.1.3.95 IUBMB
Gene Name(s): MT-CO2 Gene View COII COXII MTCO2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 3 N 261 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): MT-CO3 Gene View COIII COXIII MTCO3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1, MITOCHONDRIAL O 147 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX4I1 Gene View COX4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 5A, MITOCHONDRIAL P 109 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL Q 98 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB R 84 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6A2 Gene View COX6A
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 6B1 S 85 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6B1 Gene View COX6B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 6C T 73 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6C Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 7A1, MITOCHONDRIAL U 59 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7A1 Gene View COX7A COX7AH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 7B, MITOCHONDRIAL V 56 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 7C, MITOCHONDRIAL W 47 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7C Gene View COX7CP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 8B, MITOCHONDRIAL X 46 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX8B COX8H
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C Y 104 Bos taurus Gene Name(s): CYCS Gene View CYC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L, m 474 Escherichia coli EC#: 1.6.5.3 IUBMB
Details: SUBUNIT NUOL (CHAIN5)
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M, n 391 Escherichia coli EC#: 1.6.5.3 IUBMB
Details: SUBUNIT NUOM (CHAIN4)
NADH-QUINONE OXIDOREDUCTASE SUBUNIT N o 378 Escherichia coli EC#: 1.6.5.3 IUBMB
Details: SUBUNIT NUON (CHAIN2)
NADH-QUINONE OXIDOREDUCTASE SUBUNIT K p 281 Escherichia coli EC#: 1.6.5.3 IUBMB
Details: SUBUNITS NUOA, J AND K (CHAIN3,6 AND 4L)

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)

Protein Name: Cytochrome C Oxidase, aa3


Small Molecules
Ligands 14 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDL
Query on CDL

G, d, g CARDIOLIPIN
3'-SN-GLYCEROL, (Synonym)
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEA
Query on HEA

L HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAI
Query on NAI

1 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

D, d HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C, Y, c PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SMA
Query on SMA

C, c STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMN
Query on FMN

1 FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

1, 3, 6, 8 IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UQ1
Query on UQ1

C, c UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

2, 3, E, e FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

Q ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

L, M COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

7 CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

1, 2, 3, 4, 5, L MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
m, n, o, p L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.0 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-02
  • Released Date: 2011-10-19
  • Deposition author(s): Althoff, T., Mills, D.J., Popot, J.-L., Kuehlbrandt, W.

Revision History

  • 2012-03-28
    Type: Other | Details: Citation