5COD

Bovine heart complex I membrane domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.74 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.425 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.USA 112: 12087-12092

  • DOI: 10.1073/pnas.1510577112

  • 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, ...

    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;,Medical Research Council Mitochondrial Biology Unit, Cambridge, CB2 0XY, United Kingdom; jh@mrc-mbu.cam.ac.uk.,Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 5
L1, L2, L3, L4, L5, L6
606N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase chain 4
M1, M2, M3, M4, M5, M6
459N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
f1, h1, i1, f2, h2, i2, f3, h3, i3, f4, h4, i4, f5, h5, i5, f6, h6, i6
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
g1, g2, g3, g4, g5, g6
22N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
j1, k1, p1, s1, j2, k2, p2, s2, j3, k3, p3, s3, j4, k4, p4, s4, j5, k5, p5, s5, j6, k6, p6, s6
28N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
l1, l2, l3, l4, l5, l6
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
SDAP
U1, U2, U3, U4, U5, U6
88N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
n1, n2, n3, n4, n5, n6
59N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
o1, o2, o3, o4, o5, o6
21N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
t1, t2, t3, t4, t5, t6
57N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
u1, u2, u3, u4, u5, u6
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
v1, v2, v3, v4, v5, v6
32N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
w1, w2, w3, w4, w5, w6
27N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Unknown structure
BA, BB, BC, BD, BE, BF
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BA, BB, BC, BD, BE, BF, f1, f2, f3, f4, f5, f6, g1, g2, g3, g4, g5, g6, h1, h2, h3, h4, h5, h6, i1, i2, i3, i4, i5, i6, j1, j2, j3, j4, j5, j6, k1, k2, k3, k4, k5, k6, l1, L1, l2, L2, l3, L3, l4, L4, l5, L5, l6, L6, M1, M2, M3, M4, M5, M6, n1, n2, n3, n4, n5, n6, o1, o2, o3, o4, o5, o6, p1, p2, p3, p4, p5, p6, s1, s2, s3, s4, s5, s6, t1, t2, t3, t4, t5, t6, u1, U1, u2, U2, u3, U3, u4, U4, u5, U5, u6, U6, v1, v2, v3, v4, v5, v6, w1, w2, w3, w4, w5, w6
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.74 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.425 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 244.832α = 90.00
b = 251.414β = 90.00
c = 412.034γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOSFLMdata reduction
Cootmodel building
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references