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- PDB-8d3n: Crystal structure of human Apoptosis-Inducing Factor (AIF) comple... -

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Basic information

Entry
Database: PDB / ID: 8d3n
TitleCrystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 7-chloroquinolin-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 / 7-chloroquinolin-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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60214
Polymers118,9732
Non-polymers2,62912
Water5,098283
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8638
Polymers59,4871
Non-polymers1,3767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7396
Polymers59,4871
Non-polymers1,2525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.317, 115.223, 122.479
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 219 or (resid 220...
d_2ens_1(chain "B" and (resid 128 through 193 or (resid 194...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALASERA2 - 304
d_12ens_1ILEALAA306 - 382
d_13ens_1LYSGLNA384 - 437
d_21ens_1ALAGLNE1 - 68
d_22ens_1ASNSERE70 - 304
d_23ens_1ILEHISE307 - 433
d_24ens_1VALGLNE435 - 438

NCS oper: (Code: givenMatrix: (-0.535923035175, -0.842819960069, -0.0494066319286), (-0.843899510694, 0.536497895639, 0.00190363461624), (0.0249021328091, 0.042714434151, -0.998776932501)Vector: 37. ...NCS oper: (Code: given
Matrix: (-0.535923035175, -0.842819960069, -0.0494066319286), (-0.843899510694, 0.536497895639, 0.00190363461624), (0.0249021328091, 0.042714434151, -0.998776932501)
Vector: 37.1371773109, 19.8794942214, 45.7084570537)

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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: 59486.566 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, 295 molecules

#2: Chemical ChemComp-QBC / 7-chloroquinolin-4-amine


Mass: 178.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7ClN2 / Feature type: SUBJECT OF INVESTIGATION
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.38 M Li2SO4, 21% PEG3350, 1 mM 7-chloroquinolin-4-amine

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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: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.25→122.48 Å / Num. obs: 61990 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 41.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.042 / Rrim(I) all: 0.126 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.395 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4523 / CC1/2: 0.702 / Rpim(I) all: 0.483 / Rrim(I) all: 1.478 / % possible all: 100

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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→83.92 Å / SU ML: 0.2812 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 3040 4.91 %
Rwork0.2065 58872 -
obs0.208 61912 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.75 Å2
Refinement stepCycle: LAST / Resolution: 2.25→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 168 283 6969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236831
X-RAY DIFFRACTIONf_angle_d0.56189295
X-RAY DIFFRACTIONf_chiral_restr0.05051043
X-RAY DIFFRACTIONf_plane_restr0.00331182
X-RAY DIFFRACTIONf_dihedral_angle_d9.75062368
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.709121082921 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.31661450.28312617X-RAY DIFFRACTION99.96
2.29-2.320.35171180.2762643X-RAY DIFFRACTION99.82
2.32-2.360.29931530.25922653X-RAY DIFFRACTION99.82
2.36-2.410.29111130.24622658X-RAY DIFFRACTION99.82
2.41-2.450.27611220.24882660X-RAY DIFFRACTION99.86
2.45-2.50.25921360.24182632X-RAY DIFFRACTION99.82
2.5-2.560.30431410.22932646X-RAY DIFFRACTION99.93
2.56-2.620.24851310.21912658X-RAY DIFFRACTION99.96
2.62-2.680.2621430.2282655X-RAY DIFFRACTION99.89
2.68-2.750.27991390.23222636X-RAY DIFFRACTION99.93
2.75-2.830.27831270.22982655X-RAY DIFFRACTION99.93
2.83-2.930.28981380.23682661X-RAY DIFFRACTION99.96
2.93-3.030.25161570.22792667X-RAY DIFFRACTION99.96
3.03-3.150.2711500.23362639X-RAY DIFFRACTION99.89
3.15-3.30.24661440.21722671X-RAY DIFFRACTION99.86
3.3-3.470.25651520.20592654X-RAY DIFFRACTION99.96
3.47-3.690.26231360.20352686X-RAY DIFFRACTION99.89
3.69-3.970.22071460.18652702X-RAY DIFFRACTION99.96
3.97-4.370.18041440.15882695X-RAY DIFFRACTION100
4.37-50.16371060.15252744X-RAY DIFFRACTION99.96
5-6.30.19941390.20282763X-RAY DIFFRACTION99.97
6.3-83.920.22331600.2192877X-RAY DIFFRACTION99.9
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)
10.8795737539810.472120939213-1.65308899865E-52.887492657110.961583890550.662985909226-0.04203686242020.04762796822990.171403923735-0.0819417297540.110289829832-0.298565762402-0.1430395827980.0826927584284-0.06923487383780.344157718475-0.02056009192450.02124056527810.3700152771280.0156029731720.46273911720746.8060182916.692630947222.5954759773
22.713823883510.429785879598-0.2733177195582.415243253630.6094093518851.755523501510.0597113676932-0.119664484978-0.04081024528160.06805450399350.0091540187861-0.10551742461-0.0383936636889-0.0301794600259-0.04333311113820.331534790384-0.0105758725673-0.05259781075010.3515730035030.007695367213010.29090325066134.11928287044.1415131407628.161148614
32.4540691441-0.1921493534531.020243630492.022436528320.1769298673883.115467344040.129289445102-0.2659711800310.1353299279980.121826150992-0.1304711403130.3314036852110.219002804956-0.493454428680.007006925099140.527203244912-0.0706528468190.04366662711460.501045346676-0.03863333064120.37479975032833.000968564515.909330814447.9869445637
43.37176249742-0.3587340340030.5247976310782.36737525228-0.761230748880.7220704842170.124491183892-0.275926823071-0.5715033910150.0874416318681-0.02492499381540.1760026930290.0842996451751-0.122390379944-0.08641728535290.353843284246-0.03355826011760.01085588506530.4402851925580.06088658087060.4300240079414.9378254576-18.162368925727.3703549364
52.10274118180.08952302474940.4316039327922.01195200555-0.1922670556220.480391252290.0492834593265-0.2362790418760.1013529952840.08992078857760.0268124710250.466660501643-0.0244445158545-0.0289598575961-0.07521960275570.376206291927-0.00471544586740.01106219526240.39845758386-0.005407205780040.402651020067-3.11238703777-2.1234433037721.4286621634
60.423678737253-0.7279186185940.1572702224041.67482801351-0.5080251231981.214067740250.29874223392-0.02517775379420.248547471457-0.595765083160.155862902337-0.206973438564-0.4705459417790.490453984021-0.1256537262370.665571188316-0.2138574999810.1771143449260.443247153015-0.08067695355390.3021438661073.9437572405-1.350228631111.24809743298
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 404 )AA127 - 4041 - 277
22chain 'A' and (resid 405 through 489 )AA405 - 489278 - 362
33chain 'A' and (resid 490 through 619 )AA490 - 619363 - 437
44chain 'B' and (resid 129 through 286 )BE129 - 2862 - 159
55chain 'B' and (resid 287 through 470 )BE287 - 470160 - 344
66chain 'B' and (resid 471 through 619 )BE471 - 619345 - 438

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