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- PDB-5fs9: Crystal structure of the G338E mutant of human apoptosis inducing... -

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Basic information

Entry
Database: PDB / ID: 5fs9
TitleCrystal structure of the G338E 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: 1.75 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 31, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Derived calculations
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)114,3776
Polymers112,6222
Non-polymers1,7554
Water9,746541
1
A: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1893
Polymers56,3111
Non-polymers8782
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)57,1893
Polymers56,3111
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.619, 114.930, 121.770
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: 56310.945 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 104-613 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 104-125,531-558 AND 613-617 IN CHAIN A AND 104-125 AND 531-557 IN CHAIN B ARE DISORDERED. EACH CHAIN HAS 4 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG338E MUTATION AND 4 ADDITIONAL C-TERMINAL RESIDUES L614- V615-P616-R617 G338E MUTATION AND 4 ...G338E MUTATION AND 4 ADDITIONAL C-TERMINAL RESIDUES L614- V615-P616-R617 G338E MUTATION AND 4 ADDITIONAL C-TERMINAL RESIDUES L614- V615-P616-R617

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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: 2.83 Å3/Da / Density % sol: 56.58 % / 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: 8.2.1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→61.44 Å / Num. obs: 128212 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 99.5

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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: 1.75→114.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.867 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19995 6431 5 %RANDOM
Rwork0.17462 ---
obs0.17588 121533 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→114.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 118 541 7811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197523
X-RAY DIFFRACTIONr_bond_other_d0.0010.027296
X-RAY DIFFRACTIONr_angle_refined_deg1.441.98210210
X-RAY DIFFRACTIONr_angle_other_deg0.769316811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77523.562320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.238151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2591559
X-RAY DIFFRACTIONr_chiral_restr0.0950.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021689
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_it1.9642.6943739
X-RAY DIFFRACTIONr_mcbond_other1.9642.6923738
X-RAY DIFFRACTIONr_mcangle_it3.0224.0234678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7183.1053784
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.44.4897717
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 461 -
Rwork0.377 8875 -
obs--99.34 %
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)
10.9402-0.20280.09451.35040.25921.28150.02260.0226-0.11870.0620.0427-0.09090.22390.0724-0.06520.04150.0176-0.01060.0144-0.00190.0308-3.5554-14.758232.4351
21.6989-0.1028-0.23370.80570.20130.66140.04350.10450.08420.0343-0.02090.05180.0196-0.0904-0.02250.01960.0082-0.00050.02130.00650.0127-44.62688.022142.9523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 1002
2X-RAY DIFFRACTION2B126 - 1000

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