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- PDB-8d3k: Crystal structure of human Apoptosis-Inducing Factor (AIF) comple... -

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Basic information

Entry
Database: PDB / ID: 8d3k
TitleCrystal structure of human Apoptosis-Inducing Factor (AIF) complexed with 8-fluoro-2-methylquinolin-4-amine
Components(Apoptosis-inducing factor 1, ...) 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-fluoro-2-methylquinolin-4-amine / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)121,45512
Polymers118,9892
Non-polymers2,46610
Water4,414245
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8157
Polymers59,5031
Non-polymers1,3126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6405
Polymers59,4871
Non-polymers1,1544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.389, 115.024, 124.121
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 152 or resid 154...
d_2ens_1(chain "B" and (resid 128 through 152 or resid 154...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA2 - 26
d_12ens_1ASPLYSA29 - 67
d_13ens_1GLYLYSA71 - 128
d_14ens_1LEUALAA130 - 382
d_15ens_1GLYGLNA384 - 438
d_16ens_1C11C11B
d_21ens_1ALAALAC1 - 25
d_22ens_1ASPSERC27 - 55
d_23ens_1PROLYSC58 - 125
d_24ens_1LEUGLYC127 - 182
d_25ens_1SERHISC185 - 432
d_26ens_1VALGLNC435 - 438
d_27ens_1C11C11D

NCS oper: (Code: givenMatrix: (-0.530070383182, -0.845638696056, -0.0626145718284), (-0.847649611898, 0.530410951393, 0.0124240931509), (0.0227051606828, 0.0596608613267, -0.997960448767)Vector: 37. ...NCS oper: (Code: given
Matrix: (-0.530070383182, -0.845638696056, -0.0626145718284), (-0.847649611898, 0.530410951393, 0.0124240931509), (0.0227051606828, 0.0596608613267, -0.997960448767)
Vector: 37.3233979295, 20.0071319013, 45.8233840187)

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Components

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Apoptosis-inducing factor 1, ... , 2 types, 2 molecules AB

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


Mass: 59502.566 Da / Num. of mol.: 1
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 Apoptosis-inducing factor 1, mitochondrial / Programmed cell death protein 8


Mass: 59486.566 Da / Num. of mol.: 1
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, 255 molecules

#3: Chemical ChemComp-QC6 / 8-fluoro-2-methylquinolin-4-amine


Mass: 176.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9FN2 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.66 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 0.36 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: 1.1159 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: 2.3→124.12 Å / Num. obs: 58766 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 42.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4468 / CC1/2: 0.939 / Rpim(I) all: 0.199 / Rrim(I) all: 0.735 / % possible all: 99.8

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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: 2.3→71.55 Å / SU ML: 0.2383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 2957 5.04 %
Rwork0.1893 55730 -
obs0.1909 58687 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 161 245 6949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266853
X-RAY DIFFRACTIONf_angle_d0.59939320
X-RAY DIFFRACTIONf_chiral_restr0.05111049
X-RAY DIFFRACTIONf_plane_restr0.00351179
X-RAY DIFFRACTIONf_dihedral_angle_d9.89482390
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.888377043016 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.25641300.22872613X-RAY DIFFRACTION99.78
2.34-2.380.25021240.21742612X-RAY DIFFRACTION99.78
2.38-2.420.25851390.2182620X-RAY DIFFRACTION99.86
2.42-2.470.26141340.23292638X-RAY DIFFRACTION99.86
2.47-2.520.26681290.21562619X-RAY DIFFRACTION99.85
2.52-2.570.28481280.20692635X-RAY DIFFRACTION99.75
2.57-2.630.23711260.1952651X-RAY DIFFRACTION99.86
2.63-2.70.23761190.20292641X-RAY DIFFRACTION99.82
2.7-2.770.23361260.19472658X-RAY DIFFRACTION99.89
2.77-2.850.25981390.19892615X-RAY DIFFRACTION99.82
2.85-2.950.22651600.21022627X-RAY DIFFRACTION99.75
2.95-3.050.24811570.21552616X-RAY DIFFRACTION99.89
3.05-3.170.25851440.22642626X-RAY DIFFRACTION99.96
3.17-3.320.261560.20532634X-RAY DIFFRACTION99.82
3.32-3.490.23351470.19772664X-RAY DIFFRACTION99.96
3.49-3.710.23771310.19112669X-RAY DIFFRACTION99.96
3.71-40.20951580.17772646X-RAY DIFFRACTION99.96
4-4.40.18261330.14682695X-RAY DIFFRACTION99.93
4.4-5.040.16521590.14052689X-RAY DIFFRACTION100
5.04-6.340.1881400.1862728X-RAY DIFFRACTION100
6.35-71.550.21481780.20522834X-RAY DIFFRACTION99.67
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)
11.783171966010.61337071529-0.1747025739313.072463364891.151736080951.63198838684-0.004179329411220.0466657568576-0.01536505771070.02008064549210.184364427897-0.737921064619-0.1145176020550.131806808937-0.1626279430970.268648573645-0.000342959622764-0.0222790313320.290440925077-0.05959204824130.42342136073350.62462290563.7955360857623.6156449739
21.24695780517-0.446800852793-0.06658087653612.762887451471.687646255951.32517463865-0.006586777838280.1172719007940.092753578501-0.1849148138970.111358129834-0.596481227736-0.1435126285080.0750258295567-0.08166562339620.350481279963-0.03093687150650.08065818102430.3801354005530.006175282653510.36960129526447.76422778635.6245307460617.5793029909
32.89615973518-0.379093729105-0.8409977756373.270160475490.2002723764461.57927654741-0.048995494828-0.07559235104090.197891548593-0.08572288454050.0957835733481-0.122184306156-0.123394895740.169473303427-0.06096704679780.410272512405-0.0493332983730.01934775903860.325468571851-0.02102370193670.47991838881645.524663824530.381198986429.7452902677
41.657334488961.133388362240.1738710335812.919165780080.05049130217760.9515576264010.0006718648637320.0175137078150.1568424261090.0545146348680.0426690166965-0.000813556306077-0.0935694896977-0.0280364679433-0.03873443397680.3351219373010.0296056431651-0.03887998828010.347540140241-0.02065160979870.24748570859835.983538025112.341301252125.8764021364
52.82913858198-0.7927916854381.112946056743.220439776130.7870225418764.148917465590.101548030938-0.250579987013-0.004969115890040.2159878089020.004495834654370.529640722758-0.00760662593502-0.461551438722-0.09082278179960.489397956087-0.03285266820570.07966503796640.5121794221940.067816068850.42742673279133.512305633215.382614438648.4557606678
60.3991196879330.1495280212480.4059433956151.5503145957-2.148004424484.09639535117-0.46740864059-0.2560892692950.418918304452-0.5279174543470.1333656272020.454436903307-0.5040983244770.4330350460080.3163457386380.957741263490.441949189547-0.1770270544711.694955534060.1154074550340.6323227964327.715750896426.479515933549.9165133626
73.84084952798-0.8713731691050.2691238981462.15259518022-0.6925358093940.729173270880.108230732432-0.271209764786-0.7938924133750.0465389824193-0.01086471941690.241134940830.106695286339-0.0702154760822-0.1070503908090.37320522925-0.0192676015810.007820344645820.4086292303280.07667425423690.47216071596.08861435111-19.043848984327.6384594796
82.14372769207-0.435617830833-0.7099448607534.397693065460.1619246924061.822734802850.0692361627369-0.1538957903920.0248240150963-0.06003302285980.0923756139980.746924119473-0.02037975585780.0306359653117-0.1627959059610.327890386316-0.002974277818660.01628551614030.4482328579690.07161092488330.615476184573-14.041528187-4.6020714150321.6185625544
93.33883724141-0.06885615266350.37604951291.59075428768-0.1548627359480.3414168276470.0684900561513-0.01320677794110.111971021930.05761382320850.02026612588090.308628826277-0.01616988394170.0493136116654-0.08017347457210.3360556562910.00694492621216-0.01333144970640.3352761167640.0115964087630.2932335852112.69728052772-2.1142923571720.0316129215
102.497757531480.02317531205910.2051675074732.410985309060.6886389013692.499135906750.304460908755-0.09362698707870.200891850472-0.13518979073-0.09660807004590.00990675844694-0.3877726307620.141229991818-0.2188813775720.647793490418-0.08310053788830.03236337788670.561657218801-0.03542744018950.3783475219253.261721099620.612080182859-1.51249230596
112.010580833440.495102783031-1.485022332047.40690272352-3.673510954363.75624282510.9154679496330.9616338980460.404356464165-0.364248482724-0.02134481679130.587045198405-0.207063139605-0.218637201382-0.8516830416331.074647118840.139819674529-0.06765595134450.8349260725880.001661722543560.779906650837-4.806655455839.54794540084-4.65121025786
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 190 )AA127 - 1901 - 63
22chain 'A' and (resid 191 through 279 )AA191 - 27964 - 152
33chain 'A' and (resid 280 through 368 )AA280 - 368153 - 241
44chain 'A' and (resid 369 through 489 )AA369 - 489242 - 362
55chain 'A' and (resid 490 through 611 )AA490 - 611363 - 434
66chain 'A' and (resid 616 through 619 )AA616 - 619435 - 438
77chain 'B' and (resid 128 through 279 )BC128 - 2791 - 149
88chain 'B' and (resid 280 through 345 )BC280 - 345150 - 217
99chain 'B' and (resid 346 through 490 )BC346 - 490218 - 362
1010chain 'B' and (resid 491 through 611 )BC491 - 611363 - 432
1111chain 'B' and (resid 614 through 619 )BC614 - 619433 - 438

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