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- PDB-5kvh: Crystal structure of human apoptosis-inducing factor with W196A m... -

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Basic information

Entry
Database: PDB / ID: 5kvh
TitleCrystal structure of human apoptosis-inducing factor with W196A mutation
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / Flavoprotein / Mitochondria / Cell death
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: 2.273 Å
AuthorsBrosey, C.A. / Nix, J. / Ellenberger, T. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA92584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM109591 United States
CitationJournal: Structure / Year: 2016
Title: Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.
Authors: 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.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,3745
Polymers118,7112
Non-polymers1,6633
Water12,304683
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-11 kcal/mol
Surface area35790 Å2
Unit cell
Length a, b, c (Å)89.845, 112.166, 122.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 59355.434 Da / Num. of mol.: 2 / Mutation: W196A
Source method: isolated from a genetically manipulated source
Details: Expressed as AIF(78-613). Residues L614-Q619 remain from Prescission protease cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: O95831, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 300 mM Na2SO4, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.272→60.822 Å / Num. obs: 57812 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.184 / Net I/σ(I): 10
Reflection shellResolution: 2.27→2.33 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimless0.5.17data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BUR

4bur


Resolution: 2.273→60.822 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.42 / Stereochemistry target values: ML
Details: Hydrogens were included in riding positions during refinement. FAD cofactor and glycerol geometry restraints were prepared in eLBOW using Mogul or simple optimization, respectively, and ...Details: Hydrogens were included in riding positions during refinement. FAD cofactor and glycerol geometry restraints were prepared in eLBOW using Mogul or simple optimization, respectively, and included explicitly with the refinement. Residues 78-125, 511-559, and 613-619 are disordered in chains A and B.
RfactorNum. reflection% reflection
Rfree0.2395 2824 4.95 %
Rwork0.2022 --
obs0.204 57018 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.273→60.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6699 0 112 683 7494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027033
X-RAY DIFFRACTIONf_angle_d0.4379515
X-RAY DIFFRACTIONf_dihedral_angle_d8.1174170
X-RAY DIFFRACTIONf_chiral_restr0.0451048
X-RAY DIFFRACTIONf_plane_restr0.0021212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2732-2.31240.33071090.32862400X-RAY DIFFRACTION88
2.3124-2.35440.33451390.30952690X-RAY DIFFRACTION100
2.3544-2.39970.36541300.32688X-RAY DIFFRACTION100
2.3997-2.44870.31661410.29012699X-RAY DIFFRACTION100
2.4487-2.50190.35431150.28762692X-RAY DIFFRACTION100
2.5019-2.56010.30451310.26542739X-RAY DIFFRACTION100
2.5601-2.62410.31061310.2582693X-RAY DIFFRACTION100
2.6241-2.69510.29551490.29282678X-RAY DIFFRACTION99
2.6951-2.77440.27041490.24932715X-RAY DIFFRACTION100
2.7744-2.8640.29981570.23562710X-RAY DIFFRACTION100
2.864-2.96630.28861370.21632695X-RAY DIFFRACTION100
2.9663-3.08510.25361550.21192701X-RAY DIFFRACTION100
3.0851-3.22550.23641460.19652728X-RAY DIFFRACTION100
3.2255-3.39550.23781500.1832721X-RAY DIFFRACTION100
3.3955-3.60820.21451240.18472752X-RAY DIFFRACTION100
3.6082-3.88680.19221550.1712676X-RAY DIFFRACTION98
3.8868-4.27780.17841620.15072709X-RAY DIFFRACTION99
4.2778-4.89660.1761590.13022758X-RAY DIFFRACTION100
4.8966-6.16830.22641230.17922818X-RAY DIFFRACTION100
6.1683-60.84370.25321620.21282932X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.386-0.5943-0.41382.48520.5251.53040.1438-0.02120.7266-0.0075-0.0124-0.1012-0.2540.0312-0.14620.3128-0.0366-0.01770.2863-0.05830.4545-5.69922.1746-36.0383
23.8692-1.758-0.40172.17360.3370.4947-0.051-0.22190.02030.13570.0334-0.31280.06990.08640.01490.3241-0.039-0.02090.3317-0.00590.392611.19141.7672-37.9751
32.553-0.6135-1.74441.95540.48934.18310.00250.1711-0.0498-0.19070.00410.02090.1077-0.04690.01910.2978-0.0497-0.03490.3175-0.01780.3046-8.93063.5548-51.7212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 402 )
3X-RAY DIFFRACTION3chain 'A' and (resid 403 through 611 )

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