4BV6

Refined crystal structure of the human Apoptosis inducing factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1M6I - determined by Ye, H., Cande, C., Stephanou, N.C., Jiang, S., Gurbuxani, S., Larochette, N., Daugas, E., Garrido, C., Kroemer, G., Wu, H.  

Literature

Structural Insights Into the Coenzyme Mediated Monomer-Dimer Transition of the Pro-Apoptotic Apoptosis Inducing Factor.

Ferreira, P.Villanueva, R.Martinez-Julvez, M.Herguedas, B.Marcuello, C.Fernandez-Silva, P.Cabon, L.Hermoso, J.A.Lostao, A.Susin, S.A.Medina, M.

(2014) Biochemistry 53: 4204

  • DOI: 10.1021/bi500343r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The apoptosis-inducing factor (AIF) is a mitochondrial-flavoprotein that, after cell death induction, is distributed to the nucleus to mediate chromatinolysis. In mitochondria, AIF is present in a monomer-dimer equilibrium that after reduction by NAD ...

    The apoptosis-inducing factor (AIF) is a mitochondrial-flavoprotein that, after cell death induction, is distributed to the nucleus to mediate chromatinolysis. In mitochondria, AIF is present in a monomer-dimer equilibrium that after reduction by NADH gets displaced toward the dimer. The crystal structure of the human AIF (hAIF):NAD(H)-bound dimer revealed one FAD and, unexpectedly, two NAD(H) molecules per protomer. A 1:2 hAIF:NAD(H) binding stoichiometry was additionally confirmed in solution by using surface plasmon resonance. The here newly discovered NAD(H)-binding site includes residues mutated in human disorders, and accommodation of the coenzyme in it requires restructuring of a hAIF portion within the 509-560 apoptogenic segment. Disruption of interactions at the dimerization surface by production of the hAIF E413A/R422A/R430A mutant resulted in a nondimerizable variant considerably less efficiently stabilizing charge-transfer complexes upon coenzyme reduction than WT hAIF. These data reveal that the coenzyme-mediated monomer-dimer transition of hAIF modulates the conformation of its C-terminal proapoptotic domain, as well as its mechanism as reductase. These observations suggest that both the mitochondrial and apoptotic functions of hAIF are interconnected and coenzyme controlled: a key information in the understanding of the physiological role of AIF in the cellular life and death cycle.


    Related Citations: 
    • DNA Binding is Required for the Apoptogenic Action of Apoptosis Inducing Factor.
      Ye, H.,Cande, C.,Stephanou, N.C.,Jiang, S.,Gurbuxani, S.,Larochette, N.,Daugas, E.,Garrido, C.,Kroemer, G.,Wu, H.
      (2002) Nat.Struct.Mol.Biol. 9: 680


    Organizational Affiliation

    Departamento de Bioquímica y Biología Molecular y Celular, ‡Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)-Joint Unit BIFI-IQFR (CSIC), and §Laboratorio de Microscopias Avanzadas, Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza , Zaragoza, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
A
493Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.8 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.900α = 90.00
b = 90.500β = 94.60
c = 60.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release