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- PDB-4fdc: Crystal structure of the E493V mutant of human apoptosis inducing... -

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Basic information

Entry
Database: PDB / ID: 4fdc
TitleCrystal structure of the E493V mutant of human apoptosis inducing factor (AIF)
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsAPOPTOSIS / OXIDOREDUCTASE / Rossmann Fold / mitochondrion / APPOPTOSIS
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / chromosome condensation / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / chromosome condensation / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitochondrial respiratory chain complex I assembly / cellular response to nitric oxide / FAD binding / cellular response to estradiol stimulus / response to ischemia / neuron differentiation / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / neuron apoptotic process / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / 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 / Pyridine nucleotide-disulphide oxidoreductase / 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 / Pyridine nucleotide-disulphide oxidoreductase / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSevrioukova, I.F.
CitationJournal: Am.J.Hum.Genet. / Year: 2012
Title: Cowchock syndrome is associated with a mutation in apoptosis-inducing factor.
Authors: Rinaldi, C. / Grunseich, C. / Sevrioukova, I.F. / Schindler, A. / Horkayne-Szakaly, I. / Lamperti, C. / Landoure, G. / Kennerson, M.L. / Burnett, B.G. / Bonnemann, C. / Biesecker, L.G. / ...Authors: Rinaldi, C. / Grunseich, C. / Sevrioukova, I.F. / Schindler, A. / Horkayne-Szakaly, I. / Lamperti, C. / Landoure, G. / Kennerson, M.L. / Burnett, B.G. / Bonnemann, C. / Biesecker, L.G. / Ghezzi, D. / Zeviani, M. / Fischbeck, K.H.
History
DepositionMay 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8372
Polymers56,0521
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.400, 62.700, 101.922
Angle α, β, γ (deg.)90.00, 118.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apoptosis-inducing factor 1, mitochondrial / Programmed cell death protein 8


Mass: 56051.707 Da / Num. of mol.: 1 / Fragment: UNP residues 103-613 / Mutation: E493V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIF, AIFM1, PDCD8 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95831, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 8.5
Details: 30% PEG 1500, 0.1 M TrisHCl pH 8.5, 4% acetone, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→39.5 Å / Num. all: 21475 / Num. obs: 20005 / % possible obs: 94.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 84.9 Å2 / Rmerge(I) obs: 0.45 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.462 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3224 / % possible all: 88.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6I

1m6i


Resolution: 2.4→39.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 29.854 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29678 1082 5.1 %RANDOM
Rwork0.2532 ---
obs0.25548 20005 94.18 %-
all-21475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0.08 Å2
2--0.5 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 53 0 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193674
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9824976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72323.442154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12615628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9411529
X-RAY DIFFRACTIONr_chiral_restr0.0820.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212747
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 68 -
Rwork0.324 1308 -
obs--88.66 %
Refinement TLS params.Method: refined / Origin x: -11.8306 Å / Origin y: 2.697 Å / Origin z: -25.6071 Å
111213212223313233
T0.369 Å2-0.2934 Å2-0.0224 Å2-0.3401 Å20.0879 Å2--0.2269 Å2
L2.9765 °21.186 °20.4006 °2-0.8914 °2-0.0266 °2--0.908 °2
S-0.5413 Å °0.617 Å °0.1801 Å °-0.2498 Å °0.4488 Å °0.0845 Å °-0.0338 Å °0.0268 Å °0.0925 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B128 - 610
2X-RAY DIFFRACTION1B1000

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