5KVI

Crystal structure of monomeric human apoptosis-inducing factor with E413A/R422A/R430A mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.

Brosey, C.A.Ho, C.Long, W.Z.Singh, S.Burnett, K.Hura, G.L.Nix, J.C.Bowman, G.R.Ellenberger, T.Tainer, J.A.

(2016) Structure 24: 2067-2079

  • DOI: 10.1016/j.str.2016.09.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex ( ...

    Apoptosis-inducing factor (AIF) is critical for mitochondrial respiratory complex biogenesis and for mediating necroptotic parthanatos; these functions are seemingly regulated by enigmatic allosteric switching driven by NADH charge-transfer complex (CTC) formation. Here, we define molecular pathways linking AIF's active site to allosteric switching regions by characterizing dimer-permissive mutants using small-angle X-ray scattering (SAXS) and crystallography and by probing AIF-CTC communication networks using molecular dynamics simulations. Collective results identify two pathways propagating allostery from the CTC active site: (1) active-site H454 links to S480 of AIF's central β-strand to modulate a hydrophobic border at the dimerization interface, and (2) an interaction network links AIF's FAD cofactor, central β-strand, and Cβ-clasp whereby R529 reorientation initiates C-loop release during CTC formation. This knowledge of AIF allostery and its flavoswitch mechanism provides a foundation for biologically understanding and biomedically controlling its participation in mitochondrial homeostasis and cell death.


    Organizational Affiliation

    Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: cabrosey@mdanderson.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis-inducing factor 1, mitochondrial
A
543Homo sapiensMutation(s): 3 
Gene Names: AIFM1 (AIF, PDCD8)
EC: 1.1.1.-
Find proteins for O95831 (Homo sapiens)
Go to Gene View: AIFM1
Go to UniProtKB:  O95831
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.995 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.623α = 90.00
b = 81.802β = 90.00
c = 108.323γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesP01-CA92584
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32-GM109591

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence