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 
  • R-Value Observed: 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 U S A 112: 12087-12092

  • DOI: 10.1073/pnas.1510577112
  • Primary Citation of 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 ...

    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; jh@mrc-mbu.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5A [auth L1], T [auth L2], MA [auth L3], FB [auth L4], YB [auth L5], RC [auth L6]606Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4B [auth M1], U [auth M2], NA [auth M3], GB [auth M4], ZB [auth M5], SC [auth M6]459Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structure30Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureD [auth g1], W [auth g2], PA [auth g3], IB [auth g4], BC [auth g5], UC [auth g6]22Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structure28Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureI [auth l1], BA [auth l2], UA [auth l3], NB [auth l4], GC [auth l5], ZC [auth l6]13Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
SDAPJ [auth U1], CA [auth U2], VA [auth U3], OB [auth U4], HC [auth U5], AD [auth U6]88Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureK [auth n1], DA [auth n2], WA [auth n3], PB [auth n4], IC [auth n5], BD [auth n6]59Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureL [auth o1], EA [auth o2], XA [auth o3], QB [auth o4], JC [auth o5], CD [auth o6]21Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureO [auth t1], HA [auth t2], AB [auth t3], TB [auth t4], MC [auth t5], FD [auth t6]57Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureP [auth u1], IA [auth u2], BB [auth u3], UB [auth u4], NC [auth u5], GD [auth u6]15Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureQ [auth v1], JA [auth v2], CB [auth v3], VB [auth v4], OC [auth v5], HD [auth v6]32Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureR [auth w1], KA [auth w2], DB [auth w3], WB [auth w4], PC [auth w5], ID [auth w6]27Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown structureS [auth BA], LA [auth BB], EB [auth BC], XB [auth BD], QC [auth BE], JD [auth BF]146Bos taurusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

View Full Validation Report




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