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- PDB-8d3j: Crystal structure of human Apoptosis-Inducing Factor (AIF) comple... -

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Basic information

Entry
Database: PDB / ID: 8d3j
TitleCrystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 6-fluoro-2-methylquinolin-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 / 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 / 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-fluoro-2-methylquinolin-4-amine / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)121,40712
Polymers118,9412
Non-polymers2,46610
Water3,099172
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7837
Polymers59,4711
Non-polymers1,3126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6245
Polymers59,4711
Non-polymers1,1544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.466, 115.320, 123.974
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 129 through 219 or (resid 220...
d_2ens_1(chain "B" and (resid 129 through 152 or (resid 153...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLYA3 - 333
d_12ens_1LEUALAA336 - 381
d_13ens_1GLYGLNA383 - 437
d_21ens_1PROGLYE1 - 181
d_22ens_1SERGLYE184 - 333
d_23ens_1LEUHISE335 - 431
d_24ens_1VALGLNE433 - 436

NCS oper: (Code: givenMatrix: (-0.531053456084, -0.845944460499, -0.0485818539386), (-0.846856306846, 0.531811905694, -0.00323921546118), (0.028576604701, 0.0394216528405, -0.998813952121)Vector: 37. ...NCS oper: (Code: given
Matrix: (-0.531053456084, -0.845944460499, -0.0485818539386), (-0.846856306846, 0.531811905694, -0.00323921546118), (0.028576604701, 0.0394216528405, -0.998813952121)
Vector: 37.0159750582, 20.3109201308, 46.0558177544)

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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: 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

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-QEF / 6-fluoro-2-methylquinolin-4-amine


Mass: 176.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9FN2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.34-0.38 M Li2SO4, 25-26% 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: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.4→123.97 Å / Num. obs: 51935 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 44.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Net I/σ(I): 21.7
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4431 / CC1/2: 0.896 / Rpim(I) all: 0.243 / Rrim(I) all: 0.764

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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: 2.4→84.44 Å / SU ML: 0.2717 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2144 2636 5.08 %
Rwork0.192 49228 -
obs0.1932 51864 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→84.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 161 172 6809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186785
X-RAY DIFFRACTIONf_angle_d0.51159239
X-RAY DIFFRACTIONf_chiral_restr0.04931045
X-RAY DIFFRACTIONf_plane_restr0.00281172
X-RAY DIFFRACTIONf_dihedral_angle_d9.64352346
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.813101502792 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.29761610.25142508X-RAY DIFFRACTION99.74
2.44-2.490.2641500.2432544X-RAY DIFFRACTION99.85
2.49-2.540.28371420.22262559X-RAY DIFFRACTION99.63
2.54-2.60.24541300.20482562X-RAY DIFFRACTION99.93
2.6-2.660.24591310.20232534X-RAY DIFFRACTION99.81
2.66-2.720.25561460.20562573X-RAY DIFFRACTION99.85
2.72-2.80.27631330.20742568X-RAY DIFFRACTION99.78
2.8-2.880.26921190.21012598X-RAY DIFFRACTION99.96
2.88-2.970.24121260.21992564X-RAY DIFFRACTION99.63
2.97-3.080.25851200.21982596X-RAY DIFFRACTION99.89
3.08-3.20.22351310.22252592X-RAY DIFFRACTION99.82
3.2-3.350.21321320.21072578X-RAY DIFFRACTION99.93
3.35-3.520.22421390.20722575X-RAY DIFFRACTION99.78
3.52-3.750.24231500.19062585X-RAY DIFFRACTION99.96
3.75-4.030.20981560.18062593X-RAY DIFFRACTION99.85
4.03-4.440.16041440.14912616X-RAY DIFFRACTION99.93
4.44-5.080.15371570.14682613X-RAY DIFFRACTION99.93
5.08-6.40.20221500.19632661X-RAY DIFFRACTION100
6.4-84.440.21271190.19442809X-RAY DIFFRACTION99.8
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)
11.781299361840.842785394259-0.3710051244294.500627618891.430923062062.14941504148-0.0517145268663-0.060837955823-0.08319292755610.01484049687610.205245577421-0.766923416334-0.00741449374360.190671395274-0.2077030944760.3059227992760.0191466071177-0.01093684616910.385329532491-0.05434211583940.49510741901153.35984108233.4371435114824.0829703129
21.07302768655-0.279915180570.06715523905542.230618519061.011631630281.19973041355-0.01035625202270.1663947878860.234067756507-0.288709979619-0.0526268126671-0.211125916368-0.406652483195-0.01540950488060.06191524224880.4907979540110.01477680496160.04253735788440.4625364235790.01396077749410.36970997693342.22674743189.4789587611512.8427515066
33.33101793602-0.356000602545-0.9953950184233.37172189929-0.1444838267552.405045586280.0245080084528-0.05081682505230.261325848203-0.0011801623070.0928486662664-0.112030575837-0.187399032680.163963530832-0.1400067320880.449730127122-0.05712469827030.00400877928480.37066115502-0.02391067215520.54065561857945.34696763331.091645290830.8502531145
41.504616297090.2001434283280.8618324640963.881037551991.009880479741.47657511764-0.1573368138570.2133050230130.416841805466-0.2331854144730.214566982160.146139635924-0.2927815618790.013292980756-0.05747280583530.5337673441880.00720149427609-0.02949393771170.4169316899740.09555257103750.52462641054140.513896384334.101584547618.8107801777
52.207604806130.647234441844-0.3585206092083.06579837817-0.004395514300841.410839446590.117003939953-0.0365364515108-0.02846081507780.1517426801980.0181517298033-0.107129049642-0.01892329403780.125909152194-0.1122416384770.322288126810.0239187751378-0.02894769115430.353948469879-0.036213371110.23169389457134.47236662944.2951871515528.7042213323
64.48751716159-0.3615709846362.721510385524.127784014950.6980330313254.793359520550.0224385153416-0.1992235156150.01276518573530.1600127066790.0743595384750.6878775931590.0679860202966-0.573125377949-0.1005134973920.461228721947-0.01742918267740.09165511771180.477574329210.07859262973410.35331703819232.975111326416.305167516848.4323609964
72.97269680638-0.6349142457990.2927609318761.43895651866-0.3735423510790.3077274737390.0867165363266-0.330808493842-0.425156616022-0.004517016791140.04580020373070.2772501543470.0192347315062-0.0740394521309-0.141977371040.390584097996-0.00885956170270.02239351795140.4513131583110.01777002494210.472550331582-3.38922712307-10.320883127524.9625144737
83.57969473882-0.1695080489520.5046338174431.22255183545-0.6921213828421.43383600880.01524851482160.243864633018-0.307864920218-0.03883258096730.0025331995818-0.01504578026270.0665286383237-0.0189641422733-0.004050853620220.439030579310.00897064383939-0.03900079822660.478470047854-0.05134310148880.34584421440512.6319260007-5.4676374252517.62877238
93.39548172284-0.603660251860.4254202823833.998309365550.7882181089982.559930590430.1571787130130.1279314428640.323314618761-0.3699771673160.03196039880580.0389020759282-0.634518754250.375278653627-0.1875838895780.733813869462-0.1073594886130.1232463904630.54221578294-0.06117796236260.3489762842173.162549790240.804657543121-3.0144335897
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 - 94
22chain 'A' and (resid 224 through 286 )AA224 - 28695 - 157
33chain 'A' and (resid 287 through 368 )AA287 - 368158 - 239
44chain 'A' and (resid 369 through 404 )AA369 - 404240 - 275
55chain 'A' and (resid 405 through 490 )AA405 - 490276 - 362
66chain 'A' and (resid 491 through 619 )AA491 - 619363 - 437
77chain 'B' and (resid 129 through 404 )BE129 - 4041 - 275
88chain 'B' and (resid 405 through 503 )BE405 - 503276 - 374
99chain 'B' and (resid 504 through 619 )BE504 - 619375 - 436

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