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- PDB-4bv6: Refined crystal structure of the human Apoptosis inducing factor -

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Basic information

Entry
Database: PDB / ID: 4bv6
TitleRefined crystal structure of the human Apoptosis inducing factor
ComponentsAPOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / APOPTOSIS / NUCLEAR CHROMATINOLYSIS / DNA BINDING
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 / OTHER / Resolution: 1.8 Å
AuthorsMartinez-Julvez, M. / Herguedas, B. / Hermoso, J.A. / Ferreira, P. / Villanueva, R. / Medina, M.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: DNA Binding is Required for the Apoptogenic Action of Apoptosis Inducing Factor.
Authors: Ye, H. / Cande, C. / Stephanou, N.C. / Jiang, S. / Gurbuxani, S. / Larochette, N. / Daugas, E. / Garrido, C. / Kroemer, G. / Wu, H.
History
DepositionJun 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
Remark 0THIS ENTRY 4BV6 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1M6ISF) ...THIS ENTRY 4BV6 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1M6ISF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I:

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8223
Polymers53,9441
Non-polymers8782
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.900, 90.500, 60.500
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 53944.258 Da / Num. of mol.: 1 / Fragment: RESIDUES 121-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95831, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.25 %
Description: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA 1M6I.MTZ DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I. H.YE,C.CANDE,N.C. STEPHANOU, S.JIANG, S.GURBUXANI,N. ...Description: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA 1M6I.MTZ DETERMINED BY AUTHORS OF THE PDB ENTRY 1M6I. H.YE,C.CANDE,N.C. STEPHANOU, S.JIANG, S.GURBUXANI,N.LAROCHETTE,E. DAUGAS, C.GARRIDO, G.KROEMER, H.WU

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.8→33.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.574 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 546-557 ARE DISORDERED. AUTHOR USED THE SF DATA FROM ENTRY 1M6I
RfactorNum. reflection% reflectionSelection details
Rfree0.21526 2846 6 %RANDOM
Rwork0.19389 ---
obs0.19518 44509 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0.23 Å2
2--0.15 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 59 289 3975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9855128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82223.481158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66215656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9331530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212826
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 178 -
Rwork0.239 2420 -
obs--70.67 %

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