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- PDB-4bur: Crystal structure of the reduced human Apoptosis inducing factor ... -

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Basic information

Entry
Database: PDB / ID: 4bur
TitleCrystal structure of the reduced human Apoptosis inducing factor complexed with NAD
ComponentsAPOPTOSIS INDUCING FACTOR 1, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / APOPTOSIS / MITOCHONDRIA / NUCLEAR CHROMATINOLYSIS / DNA-BINDING / FLAVOPROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / mitochondrial disulfide relay system / cellular response to aldosterone / mitochondrial respiratory chain complex assembly / protein import into mitochondrial intermembrane space / poly-ADP-D-ribose binding / NAD(P)H oxidase H2O2-forming activity / positive regulation of necroptotic process / response to L-glutamate / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / FAD binding / cellular response to nitric oxide / response to ischemia / cellular response to estradiol stimulus / mitochondrial intermembrane space / response to toxic substance / cellular response to hydrogen peroxide / neuron differentiation / positive regulation of neuron apoptotic process / cellular response to hypoxia / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / nucleus / cytoplasm / cytosol
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 ...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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsMartinez-Julvez, M. / Herguedas, B. / Hermoso, J.A. / Ferreira, P. / Villanueva, R. / Medina, M.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Insights Into the Coenzyme Mediated Monomer-Dimer Transition of the Pro-Apoptotic Apoptosis Inducing Factor.
Authors: Ferreira, P. / Villanueva, R. / Martinez-Julvez, M. / Herguedas, B. / Marcuello, C. / Fernandez-Silva, P. / Cabon, L. / Hermoso, J.A. / Lostao, A. / Susin, S.A. / Medina, M.
History
DepositionJun 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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 / software / struct_ncs_dom_lim / 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 / _software.name / _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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,63517
Polymers223,0894
Non-polymers8,54613
Water43224
1
A: APOPTOSIS INDUCING FACTOR 1, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8854
Polymers55,7721
Non-polymers2,1123
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)57,8854
Polymers55,7721
Non-polymers2,1123
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)57,8854
Polymers55,7721
Non-polymers2,1123
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)57,9815
Polymers55,7721
Non-polymers2,2084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.766, 120.766, 343.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASNAA128 - 60926 - 507
21ALAALAASNASNBB128 - 60926 - 507
12ALAALAHISHISAA128 - 61126 - 509
22ALAALAHISHISCC128 - 61126 - 509
13ALAALAHISHISAA128 - 61126 - 509
23ALAALAHISHISDD128 - 61126 - 509
14LYSLYSILEILEBB127 - 61025 - 508
24LYSLYSILEILECC127 - 61025 - 508
15ALAALAILEILEBB128 - 61026 - 508
25ALAALAILEILEDD128 - 61026 - 508
16ALAALAHISHISCC128 - 61126 - 509
26ALAALAHISHISDD128 - 61126 - 509

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.87408, -0.48415, -0.0398), (-0.4746, 0.83362, 0.28254), (-0.10362, 0.26585, -0.95843)66.01836, 38.94597, -148.03976
2given(-0.99175, 0.03456, -0.12341), (-0.00496, -0.97257, -0.23257), (-0.12807, -0.23004, 0.96472)124.31247, -120.62219, -6.16794
3given(0.88083, 0.44753, 0.15448), (0.45723, -0.88876, -0.03234), (0.12283, 0.09912, -0.98747)75.09617, -121.54403, -167.842
4given(0.88197, 0.45645, 0.11742), (0.44334, -0.88801, 0.12202), (0.15997, -0.05556, -0.98556)10.15357, -123.59381, -183.31473
5given(-0.99964, 0.02065, -0.01692), (-0.01309, -0.93135, -0.3639), (-0.02327, -0.36355, 0.93128)70.36703, -143.39383, -26.69025
6given(-0.8903, -0.45442, -0.02954), (-0.44542, 0.85552, 0.26399), (-0.09469, 0.24819, -0.96407)68.92381, 36.38877, -149.65079

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Components

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


Mass: 55772.293 Da / Num. of mol.: 4 / Fragment: RESIDUES 103-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95831, Oxidoreductases
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.47 Å3/Da / Density % sol: 64.63 % / Description: NONE
Crystal growDetails: 16-20% PEG 4K, 0.2 M LI2SO4 AND 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626
DetectorDate: Nov 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.87→343.36 Å / Num. obs: 66707 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6I

1m6i


Resolution: 2.88→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.049 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.966 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES 517-550 IN CHAIN A, 517-552 IN CHAIN B, 518-557 IN CHAIN C AND 510-558 IN CHAIN D ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 4786 7.2 %RANDOM
Rwork0.17634 ---
obs0.18014 61636 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.685 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20.81 Å20 Å2
2--1.63 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.88→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13769 0 569 24 14362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.01419933
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98951773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55723.438608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.431152435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.54515112
X-RAY DIFFRACTIONr_chiral_restr0.10.22217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110906
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A5330.08
12B5330.08
21A5210.09
22C5210.09
31A5100.09
32D5100.09
41B5360.06
42C5360.06
51B5160.05
52D5160.05
61C5250.08
62D5250.08
LS refinement shellResolution: 2.881→2.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 317 -
Rwork0.291 4148 -
obs--99.73 %

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