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- PDB-8vgy: Crystal structure of human apoptosis-inducing factor (AIF) bound ... -

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Basic information

Entry
Database: PDB / ID: 8vgy
TitleCrystal structure of human apoptosis-inducing factor (AIF) bound to the fused N-terminal domain of CHCHD4
ComponentsApoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40
KeywordsOXIDOREDUCTASE / Apoptosis-inducing factor (AIF) / CHCHD4 / Mia40 / disulfide relay
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 / Mitochondrial protein import / response to L-glutamate ...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 / Mitochondrial protein import / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / 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 / cytosol / cytoplasm
Similarity search - Function
Mitochondrial intermembrane space import and assembly protein 40 / 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 / CHCH / CHCH domain / Pyridine nucleotide-disulphide oxidoreductase ...Mitochondrial intermembrane space import and assembly protein 40 / 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 / CHCH / CHCH domain / Pyridine nucleotide-disulphide oxidoreductase / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial / Mitochondrial intermembrane space import and assembly protein 40
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
Cancer Prevention and Research Institute of Texas (CPRIT)RP180813 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
Other privateRobert A. Welch Chemistry Chair
CitationJournal: Embo J. / Year: 2025
Title: NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism.
Authors: Brosey, C.A. / Shen, R. / Tainer, J.A.
History
DepositionDec 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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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,Mitochondrial intermembrane space import and assembly protein 40
C: Apoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2346
Polymers124,5392
Non-polymers1,6954
Water6,990388
1
A: Apoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1794
Polymers62,2691
Non-polymers9103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Apoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0552
Polymers62,2691
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.608, 109.197, 174.632
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

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Components

#1: Protein Apoptosis-inducing factor 1, mitochondrial,Mitochondrial intermembrane space import and assembly protein 40


Mass: 62269.453 Da / Num. of mol.: 2
Fragment: Fusion construct consisting of AIF followed by a linker and then residues 1-45 of Mitochondrial intermembrane space import and assembly protein 40 (CHCHD4)
Mutation: W196A in Apoptosis-inducing factor 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8, CHCHD4, MIA40 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 / Strain (production host): RosettaGami(DE3)
References: UniProt: O95831, UniProt: Q8N4Q1, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES, pH 8.0, 0.1 M NaCl,18% 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: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.3→92.6 Å / Num. obs: 59115 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 39.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.047 / Rrim(I) all: 0.147 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4548 / CC1/2: 0.63 / Rpim(I) all: 0.462 / Rrim(I) all: 1.453

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Processing

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

5kvh


Resolution: 2.3→92.59 Å / SU ML: 0.2469 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2117 2864 4.85 %
Rwork0.181 56242 -
obs0.1825 59106 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→92.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7064 0 114 388 7566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237323
X-RAY DIFFRACTIONf_angle_d0.54439923
X-RAY DIFFRACTIONf_chiral_restr0.04941106
X-RAY DIFFRACTIONf_plane_restr0.00341269
X-RAY DIFFRACTIONf_dihedral_angle_d13.8382642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.26261570.24252764X-RAY DIFFRACTION100
2.34-2.380.27691440.24922767X-RAY DIFFRACTION99.97
2.38-2.430.32021280.24272781X-RAY DIFFRACTION100
2.43-2.480.25061330.24512773X-RAY DIFFRACTION100
2.48-2.530.23771390.23232803X-RAY DIFFRACTION100
2.53-2.590.29431470.21922740X-RAY DIFFRACTION99.9
2.59-2.660.22541420.21442794X-RAY DIFFRACTION100
2.66-2.730.23281350.20882793X-RAY DIFFRACTION100
2.73-2.810.24041510.20282783X-RAY DIFFRACTION99.97
2.81-2.90.2461350.20552779X-RAY DIFFRACTION99.97
2.9-30.25551420.20572812X-RAY DIFFRACTION100
3-3.120.25231510.20152791X-RAY DIFFRACTION99.97
3.12-3.260.22121410.18692804X-RAY DIFFRACTION100
3.26-3.440.23071410.18392827X-RAY DIFFRACTION100
3.44-3.650.22451590.17732779X-RAY DIFFRACTION100
3.65-3.930.18541380.16342822X-RAY DIFFRACTION100
3.93-4.330.1811490.13462839X-RAY DIFFRACTION100
4.33-4.950.13331410.12812876X-RAY DIFFRACTION99.97
4.96-6.240.18661220.16632915X-RAY DIFFRACTION99.97
6.24-92.590.20651690.19023000X-RAY DIFFRACTION99.59
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)
12.042809725990.6216122588350.5188428176842.787263948841.839068068374.799592571050.00977537371547-0.245101954459-0.1077722410640.460678629332-0.1330394388390.2729425899730.259016561133-0.2070044739060.2056040257840.352845551146-0.0421814464870.03413803139410.3339563975080.07361322030220.356820574431-45.6737.744-18.717
21.000453882520.5930353934220.3322150477712.965768000421.29091301821.699743314990.0797587216488-0.175048889972-0.2620336273680.4999052518820.00499598038412-0.2646793460790.247701317230.156785092179-0.0579468577620.4241960650120.0149468050598-0.04169522298360.3514052769280.1189430618150.408257341203-33.9843.204-18.663
30.6955218153440.2510983836010.2394032843511.85568345490.3739084724471.475350890410.0558106409331-0.221604713268-0.07264567470190.5154539753-0.0397083954371-0.2931853338620.02705458192590.0291317507186-0.06052247414510.420903294366-0.0199299079428-0.09761853030390.4327639253020.07336645355270.363679637603-26.76420.547-14.487
41.04239882617-0.291669637807-0.5610656437944.40459114962.143682290211.14140304519-0.0195666108454-0.1696135140850.0854159482770.221496594797-0.1431671301940.353736412830.0321877864063-0.1315528077590.1105736041010.294673908312-0.012175513658-0.01293885624930.3309272483690.04325361157670.265838590058-39.66321.596-28.02
52.16348219428-0.642747249858-0.7764371656375.120018411640.8619175971591.975404226830.07707009960620.0490451277780.0307287777318-0.08669259135790.009330007783680.0285702345554-0.108403478047-0.125550043585-0.03247874563180.3231181006750.0109827208299-0.02385266640870.3388633199860.01817576522470.275925307458-38.93339.334-24.79
65.215401311281.09676711318-1.486303315793.27296073009-0.05224611167542.90640418283-0.09406987852030.542767213022-0.0393911392551-0.6012503338220.141903855277-0.2105841322610.11259484831-0.202880800689-0.01969987271860.4554788901660.0166187028571-0.02050993238150.3678641077540.01085690079970.263798092216-24.29813.211-71.282
72.286811468350.3867086640280.1934404003562.004869522140.06929030256920.7331636957630.05756220472240.1500860203560.25824343343-0.2351397842550.0424770024591-0.541630668416-0.113142214620.114489215454-0.1047452370380.3490868537840.02107554010230.07429443685090.3188652144370.006139331934920.469367372869-8.66627.592-61.837
83.43540258709-0.5460487164910.006126171580642.09498734010.4613627618660.934985401350.0188306351874-0.0700173698987-0.1348466372820.0334154808590.105776833963-0.4690398613710.09783244672520.109977590862-0.1006610144850.286660265468-4.41034783583E-5-0.05223793414930.3090297202050.005571796084520.393089781196-11.7437.712-50.954
90.02539190512780.0390841074178-0.03356210329190.0742122389683-0.0160163937690.5607106144670.3285373664680.716371855811-0.521891000726-0.868850252356-1.07009572181.55511862239-1.19887291870.01676619552881.029733939380.513704875554-0.0393980988349-0.1032111644310.842686227141-0.03027353510240.81185218621613.9345.816-43.316
100.628634749635-1.34439954726-1.180998616673.430216850120.9458033906156.681594637310.07818134115610.255602345242-0.9200646721870.0606418742445-0.467186502766-0.477660978208-0.5484276517840.003701025359420.437068906910.433826953620.126315615962-0.2106242133560.685363995243-0.1533592353441.215844515799.8874.248-45.878
119.407779683-6.51639170851-4.202465321854.588881116762.901765561676.00178490044-0.3091373088470.2640378529030.5902578513250.825359580723-0.111055521846-0.479545766224-0.171492529990.02090084226540.2463172372670.415022134959-0.0685296426722-0.06493328870690.304686446821-0.02104597204060.365767009447-32.0949.66-18.781
126.359051351291.660334900283.140998735111.161574701820.4987396315641.679408221690.04631721536230.2180651106890.470441664827-0.321525608350.124090108476-0.1903283972010.2996377536790.285445046301-0.3564199862420.4593493878750.0414614799089-0.03744542327480.3539219516320.0305190807430.38538906785-46.49248.588-26.536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 127:207 )A127 - 207
2X-RAY DIFFRACTION2( CHAIN A AND RESID 208:309 )A208 - 309
3X-RAY DIFFRACTION3( CHAIN A AND RESID 310:444 )A310 - 444
4X-RAY DIFFRACTION4( CHAIN A AND RESID 445:496 )A445 - 496
5X-RAY DIFFRACTION5( CHAIN A AND RESID 497:613 )A497 - 613
6X-RAY DIFFRACTION6( CHAIN C AND RESID 127:223 )C127 - 223
7X-RAY DIFFRACTION7( CHAIN C AND RESID 224:404 )C224 - 404
8X-RAY DIFFRACTION8( CHAIN C AND RESID 405:612 )C405 - 612
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1002:1007 )C1002 - 1007
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1008:1017 )C1008 - 1017
11X-RAY DIFFRACTION11( CHAIN A AND RESID 999:1014 )A999 - 1014
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1015:1030 )A1015 - 1030

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