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- PDB-5fs7: Crystal structure of the G262S mutant of human apoptosis inducing... -

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Basic information

Entry
Database: PDB / ID: 5fs7
TitleCrystal structure of the G262S mutant of human apoptosis inducing factor
ComponentsAPOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / MITOCHONDRIA / FLAVOPROTEIN
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 / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / cellular response to aldosterone / positive regulation of necroptotic process / NADH dehydrogenase activity / 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 / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / cellular response to aldosterone / positive regulation of necroptotic process / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / chromosome condensation / response to L-glutamate / mitochondrial respiratory chain complex I assembly / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / cellular response to estradiol stimulus / response to ischemia / mitochondrial intermembrane space / neuron differentiation / 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 / cytosol / cytoplasm
Similarity search - Function
Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain ...Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSevrioukova, I.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure/Function Relations in Aifm1 Variants Associated with Neurodegenerative Disorders.
Authors: Sevrioukova, I.F.
History
DepositionDec 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)114,1094
Polymers112,5382
Non-polymers1,5712
Water19,4381079
1
A: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0542
Polymers56,2691
Non-polymers7861
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)57,0542
Polymers56,2691
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.410, 114.570, 120.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL / / PROGRAMMED CELL DEATH PROTEIN 8 / APOPTOSIS INDUCING FACTOR


Mass: 56268.914 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 103-613 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 104-125,522-558 AND 613-617 IN CHAIN A AND 104-126,522-559 AND 614-617 IN CHAIN B ARE DISORDERED. BOTH CHAINS HAVE ADDITIONAL C-TERMINAL RESIDUES L614-V615-P616-R617, PART OF THE THROMBIN CLEAVAGE SITE.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O95831, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1079 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG262S MUTATION AND 4 ADDITIONAL RESIDUES AT THE C-TERMINUS ARE PART OF THE THROMBIN CLEAVAGE SITE ...G262S MUTATION AND 4 ADDITIONAL RESIDUES AT THE C-TERMINUS ARE PART OF THE THROMBIN CLEAVAGE SITE G262S MUTATION AND 4 ADDITIONAL RESIDUES AT THE C-TERMINUS

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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: 2.82 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M LITHIUM SULFATE, 0.1M TRIS, PH 8.5, AND 25% POLY-ETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→83.13 Å / Num. obs: 106911 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FS8

5fs8


Resolution: 1.85→114.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.569 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21691 5232 4.9 %RANDOM
Rwork0.17885 ---
obs0.18072 101544 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---20 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→114.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6952 0 106 1079 8137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197327
X-RAY DIFFRACTIONr_bond_other_d0.0010.027113
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.989955
X-RAY DIFFRACTIONr_angle_other_deg0.764316382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02523.548310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511556
X-RAY DIFFRACTIONr_chiral_restr0.0850.21101
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3061.7983646
X-RAY DIFFRACTIONr_mcbond_other1.3061.7973645
X-RAY DIFFRACTIONr_mcangle_it2.1522.6854567
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8712.0513681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0942.9645375
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 358 -
Rwork0.344 7359 -
obs--97.07 %
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)
10.42640.059-0.0130.60270.14090.4933-0.00880.00770.0358-0.03150.013-0.0377-0.054-0.0053-0.00410.0169-0.0026-0.00640.03760.00280.0412-3.707714.8395-32.5839
20.670.02240.03720.37740.02930.29660.0069-0.0793-0.048-0.0176-0.01280.0354-0.006-0.01310.00590.0021-0.00660.00080.0610.00610.0479-44.9184-8.0453-42.0149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 1000
2X-RAY DIFFRACTION2B127 - 1000

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