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- PDB-1gv4: Murine apoptosis-inducing factor (AIF) -

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Basic information

Entry
Database: PDB / ID: 1gv4
TitleMurine apoptosis-inducing factor (AIF)
ComponentsPROGRAMED CELL DEATH PROTEIN 8
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / FAD / NUCLEAR PROTEIN / APOPTOSI
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes ...electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / NADH dehydrogenase activity / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / mitochondrial intermembrane space / response to oxidative stress / neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain ...Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMate, M.J. / Alzari, P.M.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The Crystal Structure of the Mouse Apoptosis-Inducing Factor Aif
Authors: Mate, M.J. / Ortiz-Lombardia, M. / Alzari, P.M. / Boitel, B. / Haouz, A. / Tello, D. / Susin, S.A. / Penninger, J. / Kroemer, G. / Alzari, P.M.
History
DepositionFeb 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROGRAMED CELL DEATH PROTEIN 8
B: PROGRAMED CELL DEATH PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7144
Polymers115,1432
Non-polymers1,5712
Water7,927440
1
A: PROGRAMED CELL DEATH PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3572
Polymers57,5711
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROGRAMED CELL DEATH PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3572
Polymers57,5711
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.270, 109.914, 114.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99998, 0.00603, -0.00151), (-0.00601, -0.99988, -0.01413), (-0.0016, -0.01412, 0.9999)
Vector: 43.343, 142.726, 1.594)

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Components

#1: Protein PROGRAMED CELL DEATH PROTEIN 8 / APOPTOSIS-INDUCING FACTOR (AIF)


Mass: 57571.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Z0X1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 43.5 % / Description: PHASE COMBINATION WITH MAD PHASES
Crystal growpH: 7.75
Details: 18% PEG MONOMETHYL ETHER 5000, 100 MM MGCL2, 50 MM HEPES PH, pH 7.75
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 %(w/v)PEG50001reservoir
280 mM1reservoirMgCl2
350 mMHEPES1reservoirpH7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorDetector: CCD / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 62596 / % possible obs: 96.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.5 / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.273

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D7Y

1d7y


Resolution: 2→15 Å / SU B: 5.03 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.183
Details: DISORDERED RESIDUES WERE MODELED USING ROTAMERS DATA BASE AND HAVE OCC=0.00 IN THE PDB
RfactorNum. reflection% reflectionSelection details
Rfree0.25742 3577 5 %RANDOM
Rwork0.21626 ---
obs0.21836 67597 96.16 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 106 440 8064
Refinement
*PLUS
Num. reflection obs: 71317 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / Rfactor Rwork: 0.24 / Rfactor obs: 0.24

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