2YBB Oxidoreductase date Mar 02, 2011
title Fitted Model For Bovine Mitochondrial Supercomplex I1iii2iv1 Particle Cryo-Em (Emd-1876)
authors T.Althoff, D.J.Mills, J.L.Popot, W.Kuehlbrandt
compound source
Molecule: Nadh-Quinone Oxidoreductase Subunit 1
Chain: 1
Synonym: Nadh Dehydrogenase I Chain 1, Ndh-1 Subunit 1
Ec: 1.6.99.5
Other_details: Nqo1 (51kda)
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 2
Chain: 2
Synonym: Nadh Dehydrogenase I Chain 2, Ndh-1 Subunit 2
Ec: 1.6.99.5
Other_details: Nqo2 (24kda)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 3
Chain: 3
Synonym: Nadh Dehydrogenase I Chain 3, Ndh-1 Subunit 3
Ec: 1.6.99.5
Other_details: Nqo3 (75kda)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 4
Chain: 4
Synonym: Nadh Dehydrogenase I Chain 4, Ndh-1 Subunit 4
Ec: 1.6.99.5
Other_details: Nqo4 (49kda)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 5
Chain: 5
Synonym: Nadh Dehydrogenase I Chain 5, Ndh-1 Subunit 5
Ec: 1.6.99.5
Other_details: Nqo5 (30kda)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 6
Chain: 6
Synonym: Nadh Dehydrogenase I Subunit 6, Ndh-1 Subunit 6
Ec: 1.6.99.5
Other_details: Nqo6 (Psst)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 15
Chain: 7
Synonym: Nadh Dehydrogenase I Chain 15, Ndh-1 Subunit 15
Ec: 1.6.99.5
Other_details: Nqo15
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Nadh-Quinone Oxidoreductase Subunit 9
Chain: 8
Synonym: Nadh Dehydrogenase I Subunit 9, Ndh-1 Subunit 9
Ec: 1.6.99.5
Other_details: Nqo9 (Tyky)
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Atcc: 27624

Molecule: Cytochrome B-C1 Complex Subunit 1, Mitochondrial
Chain: A, a
Synonym: Complex III Subunit 1, Core Protein I, Ubiquinol-C C Reductase Complex Core Protein 1;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 2, Mitochondrial
Chain: B, b
Synonym: Complex III Subunit 2, Core Protein II, Ubiquinol- Cytochrome-C Reductase Complex Core Protein 2;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B
Chain: C, c
Synonym: Complex III Subunit 3, Complex III Subunit III, Cy B-C1 Complex Subunit 3, Ubiquinol-Cytochrome-C Reductase Co Cytochrome B Subunit;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C1, Heme Protein, Mitochondrial
Chain: D, d
Fragment: Residues 85-325
Synonym: Complex III Subunit 4, Complex III Subunit Iv, Cyt C1 Complex Subunit 4, Ubiquinol-Cytochrome-C Reductase Comp Cytochrome C1 Subunit;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit Rieske, Mitochond
Chain: E, e
Synonym: Complex III Subunit 5, Cytochrome B-C1 Complex Sub Rieske Iron-Sulfur Protein, Ubiquinol-Cytochrome C Reductas Sulfur Subunit;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 7
Chain: F, f
Synonym: Complex III Subunit 7, Ubiquinol-Cytochrome C Redu Complex 14 Kda Protein, Complex III Subunit Vii;
Ec: 1.10.2.2
Mutation: Yes
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 8
Chain: G, g
Synonym: Complex III Subunit 8, Complex III Subunit Viii, U Cytochrome C Reductase Complex 9.5 Kda Protein, Ubiquinol-C C Reductase Complex Ubiquinone-Binding Protein Qp-C;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 6, Mitochondrial
Chain: H, h
Synonym: Complex III Subunit 6, Complex III Subunit Viii, C C1 Non-Heme 11 Kda Protein, Mitochondrial Hinge Protein, Ub Cytochrome C Reductase Complex 11 Kda Protein;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit Rieske, Mitochond
Chain: I, I
Synonym: Complex III Subunit 5, Cytochrome B-C1 Complex Sub Rieske Iron-Sulfur Protein, Ubiquinol-Cytochrome C Reductas Sulfur Subunit, Cytochrome B-C1 Complex Subunit 11, Complex Subunit Ix, Ubiquinol-Cytochrome C Reductase 8 Kda Protein,
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 9
Chain: J, j
Synonym: Complex III Subunit 9, Complex III Subunit X, Cyto Non-Heme 7 Kda Protein, Ubiquinol-Cytochrome C Reductase Co Kda Protein;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome B-C1 Complex Subunit 10
Chain: K, k
Synonym: Complex III Subunit 10, Complex III Subunit Xi, Ub Cytochrome C Reductase Complex 6.4 Kda Protein;
Ec: 1.10.2.2
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 1
Chain: L
Synonym: Cytochrome C Oxidase Polypeptide I
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 2
Chain: M
Synonym: Cytochrome C Oxidase Polypeptide II
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 3
Chain: N
Synonym: Cytochrome C Oxidase Polypeptide III
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 4 Isoform 1, Mitocho
Chain: O
Synonym: Cytochrome C Oxidase Polypeptide Iv, Cytochrome C Subunit Iv Isoform 1, Cox Iv-1;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 5a, Mitochondrial
Chain: P
Synonym: Cytochrome C Oxidase Polypeptide Va
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 5b, Mitochondrial
Chain: Q
Synonym: Cytochrome C Oxidase Polypeptide Via, Cytochrome C Polypeptide Vb;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Polypeptide Via, Cytochrome Polypeptide Vb;
Chain: R
Synonym: Cytochrome C Oxidase Polypeptide Via-Heart, Cytoch Oxidase Polypeptide Vib, Coxviah;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 6b1
Chain: S
Synonym: Cytochrome C Oxidase Polypeptide Vii, Cytochrome C Subunit Aed, Cytochrome C Oxidase Subunit Vib Isoform 1, Co
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 6c
Chain: T
Synonym: Cytochrome C Oxidase Polypeptide Vic, Cytochrome C Subunit Sta;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 7a1, Mitochondrial
Chain: U
Synonym: Cytochrome C Oxidase Subunit Viiic, Cytochrome C O Subunit Viia-Heart, Cytochrome C Oxidase Subunit Viia-Muscl Cytochrome C Oxidase Subunit Viia-H, Cytochrome C Oxidase S Viia-M;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 7b, Mitochondrial
Chain: V
Synonym: Cytochrome C Oxidase Polypeptide Viib, Ihq
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 7c, Mitochondrial
Chain: W
Synonym: Cytochrome C Oxidase Polypeptide Viiia, Cytochrome Polypeptide Viic;
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C Oxidase Subunit 8b, Mitochondrial
Chain: X
Synonym: Cytochrome C Oxidase Polypeptide Viii-Heart, Cytoc Oxidase Subunit 8-1, Cytochrome C Oxidase Subunit 8h, Ix, V
Ec: 1.9.3.1
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Cytochrome C
Chain: Y
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Organ: Heart
Tissue: Muscle

Molecule: Nadh\: Ubiquinone Oxidoreductase, Membrane Subuni
Chain: m
Ec: 1.6.5.3
Other_details: Subunit Nuol (Chain5)
Organism_scientific: Escherichia Coli
Organism_taxid: 511693
Strain: Bl21
Atcc: Baa-1025

Molecule: Nadh\: Ubiquinone Oxidoreductase, Membrane Subuni
Chain: n
Synonym: Subunit Of Nadh\: Ubiquinone Oxidoreductase I
Ec: 1.6.5.3
Other_details: Subunit Nuom (Chain4)
Organism_scientific: Escherichia Coli
Organism_taxid: 511693
Strain: Bl21
Atcc: Baa-1025

Molecule: Nadh-Quinone Oxidoreductase Subunit N
Chain: o
Synonym: Nadh Dehydrogenase I Subunit N, Ndh-1 Subunit N
Ec: 1.6.5.3
Other_details: Subunit Nuon (Chain2)
Organism_scientific: Escherichia Coli
Organism_taxid: 511693
Strain: Bl21
Atcc: Baa-1025

Molecule: Nadh-Quinone Oxidoreductase Subunit K
Chain: p
Synonym: Nadh Dehydrogenase I Subunit K, Ndh-1 Subunit K
Ec: 1.6.5.3
Other_details: Subunits Nuoa, J And K (Chain3,6 And 4l)
Organism_scientific: Escherichia Coli
Organism_taxid: 511693
Strain: Bl21
Atcc: Baa-1025
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 19.00 Å
ligand CA, CDL, CU, FES, FMN, HEA, HEC, HEM, MG, NAI, SF4, SMA, UQ1, ZN enzyme Oxidoreductase E.C.1.6.99.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


5


6


7


8


B, b


E, e


F, f


H, h


I, i


K, k
  • ubiquinol-cytochrome-c reduc...


    • L


    M
  • cytochrome-c oxidase activit...


    • N
  • cytochrome-c oxidase activit...
  • oxidoreduction-driven active...


    • O


    P


    Q


    R


    S


    T
  • cytochrome-c oxidase activit...


    • U


    V


    W


    X


    Y


    a, A


    c, C


    d, D


    g, G


    j, J


    Primary referenceArrangement of electron transport chain components in bovine mitochondrial supercomplex I(1)III(2)IV(1)., Althoff T, Mills DJ, Popot JL, Kuhlbrandt W, EMBO J. 2011 Sep 9. doi: 10.1038/emboj.2011.324. PMID:21909073
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1470 Kb) [Save to disk]
  • Biological Unit Coordinates (2ybb.pdb1.gz) 1448 Kb
  • LPC: Ligand-Protein Contacts for 2YBB
  • CSU: Contacts of Structural Units for 2YBB
  • Retrieve 2YBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YBB from S2C, [Save to disk]
    • View 2YBB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 2YBB
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2YBB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ybb_L] [2ybb_m] [2ybb_P] [2ybb_O] [2ybb_B] [2ybb_d] [2ybb_J] [2ybb_X] [2ybb_8] [2ybb_S] [2ybb_5] [2ybb_p] [2ybb_7] [2ybb_e] [2ybb_H] [2ybb_b] [2ybb_M] [2ybb_4] [2ybb_j] [2ybb_V] [2ybb_i] [2ybb_o] [2ybb] [2ybb_Q] [2ybb_3] [2ybb_6] [2ybb_G] [2ybb_E] [2ybb_R] [2ybb_N] [2ybb_A] [2ybb_a] [2ybb_1] [2ybb_T] [2ybb_K] [2ybb_c] [2ybb_I] [2ybb_2] [2ybb_F] [2ybb_D] [2ybb_W] [2ybb_h] [2ybb_Y] [2ybb_g] [2ybb_n] [2ybb_U] [2ybb_C] [2ybb_k] [2ybb_f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2YBB: [Molybdop_Fe4S4] [NADH-G_4Fe-4S_3] [NADH_4Fe-4S ] by SMART
    • Other resources with information on 2YBB
  • Community annotation for 2YBB at PDBWiki (http://pdbwiki.org)
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