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- PDB-5miv: G307E variant of murine Apoptosis Inducing Factor in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 5miv
TitleG307E variant of murine Apoptosis Inducing Factor in complex with NAD+
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / Apoptosis Inducing Factor
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / response to L-glutamate ...electron-transferring-flavoprotein dehydrogenase activity / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / protein import into mitochondrial intermembrane space / cellular response to aldosterone / positive regulation of necroptotic process / response to L-glutamate / NADH dehydrogenase activity / apoptotic mitochondrial changes / 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 / 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 / response to oxidative stress / mitochondrial outer membrane / 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 / : / 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 / : / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSorrentino, L. / Cossu, F. / Aliverti, A. / Milani, M. / Mastrangelo, E.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural bases of the altered catalytic properties of a pathogenic variant of apoptosis inducing factor.
Authors: Sorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / Mastrangelo, E.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6986
Polymers116,8012
Non-polymers2,8984
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-17 kcal/mol
Surface area36270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 116.780, 166.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 128 - 611 / Label seq-ID: 51 - 534

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

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


Mass: 58400.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aifm1, Aif, Pdcd8 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Z0X1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 6000, 0.1 M HEPES, pH 7.0, 1 mM NADH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3.1→43.5 Å / Num. obs: 26576 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.992 / Net I/σ(I): 6.6
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 1946 / CC1/2: 0.331

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD4

3gd4


Resolution: 3.1→43.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26269 1322 5 %RANDOM
Rwork0.19795 ---
obs0.20121 25254 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 95.513 Å2
Baniso -1Baniso -2Baniso -3
1-6.99 Å20 Å20 Å2
2--0.69 Å20 Å2
3----7.68 Å2
Refinement stepCycle: 1 / Resolution: 3.1→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6833 0 194 125 7152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197185
X-RAY DIFFRACTIONr_bond_other_d00.026928
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9969744
X-RAY DIFFRACTIONr_angle_other_deg3.576315926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65823.588301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.994151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0071553
X-RAY DIFFRACTIONr_chiral_restr0.0770.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217977
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021624
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_it5.6499.3163530
X-RAY DIFFRACTIONr_mcbond_other5.6449.3153529
X-RAY DIFFRACTIONr_mcangle_it8.9413.9514402
X-RAY DIFFRACTIONr_mcangle_other8.94113.9524403
X-RAY DIFFRACTIONr_scbond_it5.2779.7823655
X-RAY DIFFRACTIONr_scbond_other5.279.7753652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.74114.4625337
X-RAY DIFFRACTIONr_long_range_B_refined13.57875.3768506
X-RAY DIFFRACTIONr_long_range_B_other13.56475.3948500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26198 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 114 -
Rwork0.434 1832 -
obs--99.79 %

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