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- PDB-3gd3: Crystal structure of a naturally folded murine apoptosis inducing... -

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Basic information

Entry
Database: PDB / ID: 3gd3
TitleCrystal structure of a naturally folded murine apoptosis inducing factor
Components(Apoptosis-inducing factor 1, mitochondrial) x 2
KeywordsOXIDOREDUCTASE / alpha and beta protein / Acetylation / Apoptosis / DNA-binding / FAD / Flavoprotein / Mitochondrion / Nucleus / Phosphoprotein / Transit peptide
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 / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / oxidoreductase activity, acting on NAD(P)H ...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 / cellular response to aldosterone / positive regulation of necroptotic process / protein import into mitochondrial intermembrane space / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / apoptotic mitochondrial changes / 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 / neuron differentiation / 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 / 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 / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSevrioukova, I.F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Redox-linked conformational dynamics in apoptosis-inducing factor
Authors: Sevrioukova, I.F.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
C: Apoptosis-inducing factor 1, mitochondrial
D: Apoptosis-inducing factor 1, mitochondrial
E: Apoptosis-inducing factor 1, mitochondrial
F: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,02310
Polymers234,8816
Non-polymers3,1424
Water48627
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1142
Polymers58,3281
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)59,1142
Polymers58,3281
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1142
Polymers58,3281
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1142
Polymers58,3281
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Apoptosis-inducing factor 1, mitochondrial


  • defined by author&software
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Apoptosis-inducing factor 1, mitochondrial


  • defined by author&software
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.050, 80.290, 419.640
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


Mass: 58328.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aif, Aifm1, Pdcd8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z0X1
#2: Protein/peptide Apoptosis-inducing factor 1, mitochondrial /


Mass: 783.958 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aif, Aifm1, Pdcd8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR STATES THAT CHAINS E AND F ARE LIKELY PARTS OF THE N-TERMINI OF CHAINS A,B,C, AND D. 48- ...THE AUTHOR STATES THAT CHAINS E AND F ARE LIKELY PARTS OF THE N-TERMINI OF CHAINS A,B,C, AND D. 48-49 N-TERMINAL RESIDUES IN ALL FOUR MOLECULES IN THE ASYMMETRIC UNIT ARE MISSING (DISORDERED). OWING TO LOW RESOLUTION, IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS AND IDENTIFY THE PEPTIDES. THE N-TERMINI WERE MODELED AS ALA, BUT THE SEQUENCE ALIGNMENT IS UNKNOWN, AND WERE THEREFORE CHANGED TO UNK IN THIS ENTRY.

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 7
Details: 15% PEG 4000, 0.35M KNO3, pH 7.0, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2008 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→408.25 Å / Num. all: 61080 / Num. obs: 49548 / % possible obs: 81.12 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.97 % / Rmerge(I) obs: 0.174 / Rsym value: 0.174
Reflection shellResolution: 2.8→2.873 Å / Redundancy: 5.06 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.715 / % possible all: 69.45

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GV4

1gv4


Resolution: 2.95→46.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.907 / SU B: 47.252 / SU ML: 0.415 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29965 2103 4.6 %RANDOM
Rwork0.24861 ---
obs0.25095 43694 83.42 %-
all-71343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.017 Å2
Baniso -1Baniso -2Baniso -3
1--6.06 Å20 Å20 Å2
2---0.65 Å20 Å2
3---6.71 Å2
Refinement stepCycle: LAST / Resolution: 2.95→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14482 0 212 27 14721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02214994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.771.97720305
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9851878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12323.721637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.869152543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.28815112
X-RAY DIFFRACTIONr_chiral_restr0.1030.22241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.26848
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.210030
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.59331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.559214970
X-RAY DIFFRACTIONr_scbond_it1.93235663
X-RAY DIFFRACTIONr_scangle_it3.1624.55335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 131 -
Rwork0.355 2869 -
obs--75.55 %
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)
11.8087-0.25430.13670.6477-0.07070.5292-0.0404-0.0571-0.09110.0306-0.0220.10.0236-0.0040.06240.07690.03090.01320.0529-0.01470.03412.337822.155358.5587
20.7702-0.0981-0.35720.8281-0.11560.6821-0.02150.116-0.0694-0.189-0.0169-0.04620.07440.0030.03840.19640.00340.01280.0798-0.05240.0409-16.39216.75516.3059
30.4489-0.18850.09961.091-0.12560.6268-0.06270.0013-0.25420.06760.00110.06220.0634-0.00780.06170.10130.03010.08410.0188-0.00160.209-34.9995-17.446844.1859
40.4939-0.0757-0.07530.62380.12050.47170.0291-0.17460.14050.218-0.06440.149-0.04790.01250.03530.2988-0.010.00310.2825-0.07430.114725.532638.841397.7615
53.13670.87120.51464.6635-0.13760.1023-0.1841-0.0587-0.3091-0.38930.27010.2473-0.0101-0.0287-0.0860.28540.08250.02710.188-0.00990.1532-8.427453.158649.0855
64.53893.30610.06315.0727-0.09320.0083-0.0655-0.0930.05360.43570.10880.6196-0.0247-0.0155-0.04330.27790.1128-0.00440.36990.12250.3534-5.229649.249555.5201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 610
2X-RAY DIFFRACTION2B127 - 610
3X-RAY DIFFRACTION3C128 - 610
4X-RAY DIFFRACTION4D128 - 610
5X-RAY DIFFRACTION5E1 - 8
6X-RAY DIFFRACTION6F1 - 9

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