5COD | pdb_00005cod

Bovine heart complex I membrane domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.74 Å
  • R-Value Free: 
    0.435 (Depositor), 0.445 (DCC) 
  • R-Value Work: 
    0.425 (Depositor), 0.425 (DCC) 
  • R-Value Observed: 
    0.425 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure of subcomplex I beta of mammalian respiratory complex I leads to new supernumerary subunit assignments.

Zhu, J.King, M.S.Yu, M.Klipcan, L.Leslie, A.G.Hirst, J.

(2015) Proc Natl Acad Sci U S A 112: 12087-12092

  • DOI: https://doi.org/10.1073/pnas.1510577112
  • Primary Citation Related Structures: 
    5COD

  • PubMed Abstract: 

    Mitochondrial complex I (proton-pumping NADH:ubiquinone oxidoreductase) is an essential respiratory enzyme. Mammalian complex I contains 45 subunits: 14 conserved "core" subunits and 31 "supernumerary" subunits. The structure of Bos taurus complex I, determined to 5-Å resolution by electron cryomicroscopy, described the structure of the mammalian core enzyme and allowed the assignment of 14 supernumerary subunits. Here, we describe the 6.8-Å resolution X-ray crystallography structure of subcomplex Iβ, a large portion of the membrane domain of B. taurus complex I that contains two core subunits and a cohort of supernumerary subunits. By comparing the structures and composition of subcomplex Iβ and complex I, supported by comparisons with Yarrowia lipolytica complex I, we propose assignments for eight further supernumerary subunits in the structure. Our new assignments include two CHCH-domain containing subunits that contain disulfide bridges between CX9C motifs; they are processed by the Mia40 oxidative-folding pathway in the intermembrane space and probably stabilize the membrane domain. We also assign subunit B22, an LYR protein, to the matrix face of the membrane domain. We reveal that subunit B22 anchors an acyl carrier protein (ACP) to the complex, replicating the LYR protein-ACP structural module that was identified previously in the hydrophilic domain. Thus, we significantly extend knowledge of how the mammalian supernumerary subunits are arranged around the core enzyme, and provide insights into their roles in biogenesis and regulation.


  • Organizational Affiliation
    • Medical Research Council Mitochondrial Biology Unit, Cambridge, CB2 0XY, United Kingdom;

Macromolecule Content 

  • Total Structure Weight: 894.12 kDa 
  • Atom Count: 48,030 
  • Modeled Residue Count: 9,606 
  • Deposited Residue Count: 10,482 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5606Bos taurusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Bos taurusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure22Bos taurusMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure13Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
SDAP88Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure59Bos taurusMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure21Bos taurusMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure57Bos taurusMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure15Bos taurusMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure32Bos taurusMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure27Bos taurusMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown structure146Bos taurusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.74 Å
  • R-Value Free:  0.435 (Depositor), 0.445 (DCC) 
  • R-Value Work:  0.425 (Depositor), 0.425 (DCC) 
  • R-Value Observed: 0.425 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.832α = 90
b = 251.414β = 90
c = 412.034γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
MOSFLMdata reduction
PHENIXrefinement
Cootmodel building
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary