Crystal structure of Tim40/MIA40, a disulfide relay system in mitochondria, solved as MBP fusion protein

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

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Structural basis of yeast Tim40/Mia40 as an oxidative translocator in the mitochondrial intermembrane space.

Kawano, S.Yamano, K.Naoe, M.Momose, T.Terao, K.Nishikawa, S.Watanabe, N.Endo, T.

(2009) Proc Natl Acad Sci U S A 106: 14403-14407

  • DOI: https://doi.org/10.1073/pnas.0901793106
  • Primary Citation of Related Structures:  
    2ZXT, 3A3C

  • PubMed Abstract: 

    The mitochondrial intermembrane space (IMS) contains many small cysteine-bearing proteins, and their passage across the outer membrane and subsequent folding require recognition and disulfide bond transfer by an oxidative translocator Tim40/Mia40 in the inner membrane facing the IMS. Here we determined the crystal structure of the core domain of yeast Mia40 (Mia40C4) as a fusion protein with maltose-binding protein at a resolution of 3 A. The overall structure of Mia40C4 is a fruit-dish-like shape with a hydrophobic concave region, which accommodates a linker segment of the fusion protein in a helical conformation, likely mimicking a bound substrate. Replacement of the hydrophobic residues in this region resulted in growth defects and impaired assembly of a substrate protein. The Cys296-Cys298 disulfide bond is close to the hydrophobic concave region or possible substrate-binding site, so that it can mediate disulfide bond transfer to substrate proteins. These results are consistent with the growth phenotypes of Mia40 mutant cells containing Ser replacement of the conserved cysteine residues.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40465Escherichia coli K-12synthetic constructSaccharomyces cerevisiae S288C
This entity is chimeric
Mutation(s): 0 
Gene Names: MIA40TIM40YKL195W
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P36046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36046 
Go to UniProtKB:  P36046
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9P36046
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.263α = 90
b = 101.403β = 90
c = 109.355γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-07-16
    Changes: Database references
  • Version 1.3: 2017-06-28
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary