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- PDB-8d3e: Crystal structure of human Apoptosis-Inducing Factor (AIF) W196A ... -

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Basic information

Entry
Database: PDB / ID: 8d3e
TitleCrystal structure of human Apoptosis-Inducing Factor (AIF) W196A mutant complexed with 6-fluoroquinolin-4-amine
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / mitochondrial import / oxidative phosphorylation / SAXS
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / 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 / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / 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 / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / cellular response to nitric oxide / response to ischemia / cellular response to estradiol stimulus / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / neuron differentiation / positive regulation of neuron apoptotic process / cellular response to hypoxia / 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 / : / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 6-fluoroquinolin-4-amine / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBrosey, C.A. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP180813 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Chemical screening by time-resolved X-ray scattering to discover allosteric probes.
Authors: Brosey, C.A. / Link, T.M. / Shen, R. / Moiani, D. / Burnett, K. / Hura, G.L. / Jones, D.E. / Tainer, J.A.
History
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)120,6048
Polymers118,7112
Non-polymers1,8936
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, The AIF-W196A mutant exists as a monomer-dimer equilibrium in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.786, 114.330, 120.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 128 through 166 or (resid 167...
d_2ens_1(chain "B" and (resid 128 through 147 or (resid 148...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAHISA1 - 433
d_12ens_1FADFADB
d_21ens_1ALAALAE3 - 384
d_22ens_1GLYHISE386 - 436
d_23ens_1FADFADF

NCS oper: (Code: givenMatrix: (-0.541170844665, -0.840435404371, -0.028327512515), (-0.840725993789, 0.54145340102, -0.00283158797341), (0.0177177947772, 0.0222833032555, -0.999594684932)Vector: -36. ...NCS oper: (Code: given
Matrix: (-0.541170844665, -0.840435404371, -0.028327512515), (-0.840725993789, 0.54145340102, -0.00283158797341), (0.0177177947772, 0.0222833032555, -0.999594684932)
Vector: -36.6596389669, -19.8894458166, -74.0543560011)

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Components

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Protein , 1 types, 2 molecules AB

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: O95831, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 362 molecules

#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-QDI / 6-fluoroquinolin-4-amine


Mass: 162.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7FN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7-8, 0.3 M Na2SO4, 16-18% PEG3350 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.38→29.34 Å / Num. obs: 50201 / % possible obs: 99.3 % / Redundancy: 10.6 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Net I/σ(I): 16.1
Reflection shellResolution: 2.38→2.46 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4275 / CC1/2: 0.852 / Rpim(I) all: 0.232 / Rrim(I) all: 0.765 / % possible all: 93

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KVH

5kvh


Resolution: 2.38→29.34 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2118 2436 4.86 %
Rwork0.1801 47695 -
obs0.1816 50131 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.46 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6523 0 127 356 7006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196790
X-RAY DIFFRACTIONf_angle_d0.51079227
X-RAY DIFFRACTIONf_chiral_restr0.04961038
X-RAY DIFFRACTIONf_plane_restr0.00281179
X-RAY DIFFRACTIONf_dihedral_angle_d10.21752399
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.497721391979 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.430.31891300.23292481X-RAY DIFFRACTION88.87
2.43-2.490.2931460.21812771X-RAY DIFFRACTION100
2.49-2.540.23421480.19492775X-RAY DIFFRACTION100
2.54-2.610.24561340.19352821X-RAY DIFFRACTION100
2.61-2.680.27151380.18892777X-RAY DIFFRACTION100
2.68-2.760.23441410.18762797X-RAY DIFFRACTION99.97
2.76-2.850.24951640.17782765X-RAY DIFFRACTION100
2.85-2.950.23581370.18242805X-RAY DIFFRACTION100
2.95-3.070.22631400.18872811X-RAY DIFFRACTION100
3.07-3.20.23181540.18862797X-RAY DIFFRACTION100
3.2-3.370.22311580.1762808X-RAY DIFFRACTION100
3.37-3.580.2141480.17652805X-RAY DIFFRACTION100
3.58-3.860.20031550.17232835X-RAY DIFFRACTION100
3.86-4.250.15471500.15392824X-RAY DIFFRACTION100
4.25-4.860.15121220.14362891X-RAY DIFFRACTION100
4.86-6.110.20291170.19232921X-RAY DIFFRACTION100
6.11-29.340.22531540.2063011X-RAY DIFFRACTION99.75
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)
12.4716181109-0.725265881633-0.3869983662860.9958696858110.312602552370.8484677491490.0685085818346-0.1989924243460.3160194443670.0516128201211-0.0148398996337-0.168097463635-0.06566005097330.12556785375-0.07041388004110.359020115437-0.0391891164357-0.01637952949410.381442162734-0.04843895551810.425233615544-0.69495302696815.9946089915-33.5381171653
26.386061482362.375778949145.800589811035.060440483862.547061499487.25612440073-0.186950571928-0.267187965412-0.272382713651-0.1480628907480.313355162257-0.216192989155-0.260957600822-0.107697973989-0.1692258642410.4683065312970.0389006303510.00709467333860.4583890039820.05382074170650.48740325332512.0477559149-4.1878241693-44.7314057878
33.21438598024-0.291260376636-0.08926634988150.843813494007-0.07581589857780.2870728705510.0542509545147-0.0356359172588-0.000229897743741-0.0277486284832-0.0249721390624-0.09945432932080.08340269035330.0399605264664-0.02304553270370.426500772271-0.002316617290880.01420341991730.3878163697290.01448998834470.331769284832-2.155596978081.97345779991-40.5268972341
45.040498110380.487253826264-1.058941053754.7903330138-0.06021007457623.341242932110.2518989308910.0907949606707-0.41781354553-0.122462498815-0.1297354373070.08812883419150.676280335066-0.158856700086-0.1108691327740.623418090874-0.0583923825431-0.1156472573640.4681539243170.01773495795620.33631165657-4.30281624410.0436126267849-61.2078352705
51.983943098410.646289057602-0.1883798140823.04260150266-1.467043548091.71901009136-0.08941188545270.04950349818450.160522742257-0.1489720469850.1659976887240.4691970953290.0533314615126-0.237525101406-0.08752997275680.332474896658-0.0182865520522-0.06409403900960.358817700272-0.01018267788150.334671637683-49.0691122148-3.0077784684-40.477766373
63.84048416995-1.344681000681.766717463283.19259679147-0.9011376857913.020751653420.04122322916030.123681280734-0.46544635033-0.370452783570.1325598321480.3252936535490.318325737829-0.222452397164-0.1584501658570.502955218942-0.0777177429254-0.02210210726920.331596879378-0.01073634588440.432022703709-44.3226293266-31.0307266351-33.7100901166
71.164490475930.8247309442050.1154718937822.840767510180.2021588525440.8975125897870.01182461316010.0776159319316-0.082101184848-0.07237042486560.02145555797830.01045858748590.169002784058-0.00485806849887-0.042173999060.373908099221-0.004226455857220.01803817036450.353765695514-0.001199923382870.272074367883-35.1882430634-12.4537704612-35.1655728029
85.18404833859-0.256819256227-1.326013228044.959431869110.08441558095533.012184775970.119739948127-0.1345089234670.04777775243480.116418687343-0.054642928104-0.2946544551330.1069379489250.253718521386-0.05762925144160.393028995644-0.0346483975797-0.0386490514830.437097083373-0.002417174396060.239876601253-32.6647477872-16.1538364611-12.859274596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 128 through 326 )AA128 - 3261 - 199
22chain 'A' and (resid 327 through 345 )AA327 - 345200 - 218
33chain 'A' and (resid 346 through 490 )AA346 - 490219 - 363
44chain 'A' and (resid 491 through 611 )AA491 - 611364 - 433
55chain 'B' and (resid 126 through 267 )BE126 - 2671 - 142
66chain 'B' and (resid 268 through 368 )BE268 - 368143 - 243
77chain 'B' and (resid 369 through 490 )BE369 - 490244 - 365
88chain 'B' and (resid 491 through 611 )BE491 - 611366 - 436

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