8VGY | pdb_00008vgy

Crystal structure of human apoptosis-inducing factor (AIF) bound to the fused N-terminal domain of CHCHD4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Literature

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism.

Brosey, C.A.Shen, R.Tainer, J.A.

(2025) EMBO J 44: 1220-1248

  • DOI: https://doi.org/10.1038/s44318-024-00360-6
  • Primary Citation of Related Structures:  
    8VGY

  • PubMed Abstract: 

    Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4's AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4's β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates. NMR and X-ray scattering (SAXS) solution measurements, mutational analyses, and biochemistry show that the substrate-mimicking AIF-interaction domain shields CHCHD4's redox-sensitive active site. Disrupting this shield critically activates CHCHD4 substrate affinity and chaperone activity. Regulatory-domain sequestration by NADH-activated AIF directly stimulates chaperone binding and folding, revealing how AIF mediates CHCHD4 mitochondrial import. These results establish AIF as an integral component of the metazoan disulfide relay and point to NADH-activated dimeric AIF as an organizational import center for CHCHD4 and its substrates. Importantly, AIF regulation of CHCHD4 directly links AIF's cellular NAD(H) sensing to CHCHD4 chaperone function, suggesting a mechanism to balance tissue-specific oxidative phosphorylation (OXPHOS) capacity with NADH availability.


  • Organizational Affiliation

    Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40A,
B [auth C]
571Homo sapiensMutation(s): 1 
Gene Names: AIFM1AIFPDCD8CHCHD4MIA40
EC: 1.6.99
UniProt & NIH Common Fund Data Resources
Find proteins for O95831 (Homo sapiens)
Explore O95831 
Go to UniProtKB:  O95831
PHAROS:  O95831
GTEx:  ENSG00000156709 
Find proteins for Q8N4Q1 (Homo sapiens)
Explore Q8N4Q1 
Go to UniProtKB:  Q8N4Q1
PHAROS:  Q8N4Q1
GTEx:  ENSG00000163528 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO95831Q8N4Q1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.608α = 90
b = 109.197β = 90
c = 174.632γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP180813
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35 CA220430
Other privateRobert A. Welch Chemistry Chair

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references