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- PDB-8d3o: Crystal structure of human Apoptosis-Inducing Factor (AIF) comple... -

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Basic information

Entry
Database: PDB / ID: 8d3o
TitleCrystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 8-methoxyquinolin-4-amine
Components(Apoptosis-inducing factor ...) x 2
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 / 8-methoxyquinolin-4-amine / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
D: Apoptosis-inducing factor (AIF), unidentified helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,30516
Polymers119,5553
Non-polymers2,75013
Water2,594144
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7817
Polymers59,4711
Non-polymers1,3106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis-inducing factor 1, mitochondrial
D: Apoptosis-inducing factor (AIF), unidentified helix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5249
Polymers60,0842
Non-polymers1,4407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.104, 115.045, 122.167
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
DetailsIt is unknown to which chain the unidentified helix belongs. Therefore, it was given the chain ID D, and included with the biological assembly of chain B.

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Components

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Apoptosis-inducing factor ... , 2 types, 3 molecules ABD

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


Mass: 59470.566 Da / Num. of mol.: 2
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 NADH or NADPH; With unknown physiological acceptors
#2: Protein/peptide Apoptosis-inducing factor (AIF), unidentified helix


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors

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Non-polymers , 5 types, 157 molecules

#3: Chemical ChemComp-QF6 / 8-methoxyquinolin-4-amine


Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 0.38 M Li2SO4, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.25→122.17 Å / Num. obs: 61381 / % possible obs: 99.6 % / Redundancy: 11.2 % / Biso Wilson estimate: 46.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Net I/σ(I): 17.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4438 / CC1/2: 0.878 / Rpim(I) all: 0.306 / Rrim(I) all: 1.03 / % possible all: 99

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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: 4BV6

4bv6


Resolution: 2.25→83.75 Å / SU ML: 0.2749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 3003 4.9 %
Rwork0.2128 58306 -
obs0.214 61309 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.61 Å2
Refinement stepCycle: LAST / Resolution: 2.25→83.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 176 144 6800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166822
X-RAY DIFFRACTIONf_angle_d0.46229299
X-RAY DIFFRACTIONf_chiral_restr0.04841050
X-RAY DIFFRACTIONf_plane_restr0.00271179
X-RAY DIFFRACTIONf_dihedral_angle_d9.2082331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.35461370.28422727X-RAY DIFFRACTION99.03
2.29-2.330.35641310.26482731X-RAY DIFFRACTION99.07
2.33-2.370.27561420.24632716X-RAY DIFFRACTION99.1
2.37-2.410.23851180.24212761X-RAY DIFFRACTION99.04
2.41-2.460.28131400.2422749X-RAY DIFFRACTION99.24
2.46-2.520.27381380.23362716X-RAY DIFFRACTION99.37
2.52-2.580.24061460.22612747X-RAY DIFFRACTION99.21
2.58-2.640.25661210.22432749X-RAY DIFFRACTION99.45
2.64-2.710.30641600.22632741X-RAY DIFFRACTION99.59
2.71-2.790.2611370.242757X-RAY DIFFRACTION99.52
2.79-2.880.29351390.24452784X-RAY DIFFRACTION99.56
2.88-2.980.28021610.24442737X-RAY DIFFRACTION99.79
2.98-3.10.28271640.2422741X-RAY DIFFRACTION99.59
3.1-3.240.26481500.23732759X-RAY DIFFRACTION99.66
3.25-3.420.24971560.21522785X-RAY DIFFRACTION99.97
3.42-3.630.23121380.21562796X-RAY DIFFRACTION99.73
3.63-3.910.23721480.19582790X-RAY DIFFRACTION99.93
3.91-4.30.20471500.17722808X-RAY DIFFRACTION100
4.3-4.930.18511210.16282861X-RAY DIFFRACTION99.93
4.93-6.210.21641400.20972866X-RAY DIFFRACTION99.9
6.21-83.750.20911660.22612985X-RAY DIFFRACTION99.84
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)
11.838817655660.954916236342-0.4310304596572.538058793211.035135876621.551583593330.0415586675456-0.101999770775-0.09171853089380.324595295220.215583640202-1.226243537140.08472318434160.171415062134-0.2483157091950.3763881998660.0154959762969-0.0675785546910.458268438858-0.08937660006930.93960824584453.15491195553.5594987694423.7372341031
20.9653774522450.6854326645690.0005914636554012.507011074940.9579762058340.60591002374-0.05263908201160.1531326133080.38168068312-0.2729484456720.0840258352731-0.253782598672-0.2696635362890.0665005548596-0.04171201885450.514222403457-0.0196493648422-0.05684712585310.4944306666560.04595442653220.69529735795640.89655247820.335835694121.524765887
30.9481692187591.057238031980.7860148837712.443343687782.220329719892.866107597620.255870895776-0.113732928295-0.002578815211560.220797106611-0.1166549501240.002558688682090.100262741005-0.083947824499-0.1215849919710.457718708288-0.0556978379672-0.03062498844930.4332905722470.04338975890420.41967791295134.903137350110.88843821341.5256967765
49.14160523903-0.3118437184669.541875412211.71298543069-0.3667770501669.95963805564-0.450044992268-1.462437442320.0357665690838-0.1784636201120.4388758473970.3893793673320.243319288462-1.67235366966-0.03060204213281.055744453830.415304530107-0.337016482951.03822948751-0.1433720147770.84689546069327.214090806726.192713124849.38960778
53.29379529175-0.2086766238450.3998313116332.6083193341-1.070887333190.4240652825490.20431835898-0.238264671342-0.7293437536910.0466905855736-0.1083186483690.3468722605920.156161482037-0.173614521612-0.07617402910680.382901084361-0.0431926821617-0.01957378137220.4962479358890.06812824292130.6071517518364.91603820277-18.42655286927.2168867767
61.88501111737-0.225559469882-0.2534763899734.175598742880.7499881295930.9227494774060.125573455789-0.3465534654760.380114031529-0.05158753191950.09040569631371.26875876413-0.0990521207157-0.0129594363019-0.1910622628480.406970653955-0.01181724439120.05680031251610.5261528839770.009950623477841.01456185889-14.7185317350.22545053952321.3726245416
73.804208080211.05264471583-0.3191831997982.28615747765-0.1358629219840.64832523812-0.08133006036740.224625926272-0.187259184004-0.05884674555160.03813765864680.08362776842570.08339403644820.1304636699680.06976814088830.387439025540.00493111642527-0.06991841211850.452507830172-0.0120432483880.40617337680413.9850090564-6.7410370555318.900689376
83.008161801390.3390511766140.1772516557991.62882514932-0.356432821530.1117900502930.679085226203-0.09959167642240.804214931294-0.4689990661630.220706705265-0.197241569445-1.037221668570.907714354468-0.3897281395320.862719856799-0.3392234371140.2089264280190.629641710137-0.111754058160.4322933740483.189584628330.71510396603-0.952642838229
96.295906284144.03502439627-3.256831878292.99420332956-0.7833091341265.82135686532-0.2641645811780.3145823011291.13627072896-0.3793097026540.825863067458-1.08713367433-1.61671715227-0.55075443344-0.4347666459441.15210139007-0.0371414313659-0.0365125790630.513975768929-0.1367082215811.33921162146-4.581021386810.1688409859-3.52977336707
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 127 through 223 )AA127 - 2231 - 95
22chain 'A' and (resid 224 through 441 )AA224 - 44196 - 314
33chain 'A' and (resid 442 through 611 )AA442 - 611315 - 434
44chain 'A' and (resid 616 through 619 )AA616 - 619435 - 438
55chain 'B' and (resid 129 through 286 )BC129 - 2862 - 159
66chain 'B' and (resid 287 through 404 )BC287 - 404160 - 279
77chain 'B' and (resid 405 through 490 )BC405 - 490280 - 366
88chain 'B' and (resid 491 through 611 )BC491 - 611367 - 435
99chain 'B' and (resid 615 through 619 )BC615 - 619436 - 440

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