[English] 日本語
Yorodumi
- PDB-5kvi: Crystal structure of monomeric human apoptosis-inducing factor wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kvi
TitleCrystal structure of monomeric human apoptosis-inducing factor with E413A/R422A/R430A mutations
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / Flavoprotein / Mitochondria Cell death
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 / molecular replacement / Resolution: 1.995 Å
AuthorsBrosey, C.A. / Nix, J. / Ellenberger, T. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA92584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM109591 United States
CitationJournal: Structure / Year: 2016
Title: Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.
Authors: Brosey, C.A. / Ho, C. / Long, W.Z. / Singh, S. / Burnett, K. / Hura, G.L. / Nix, J.C. / Bowman, G.R. / Ellenberger, T. / Tainer, J.A.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3564
Polymers59,2401
Non-polymers1,1163
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-1 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.623, 81.802, 108.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 59240.301 Da / Num. of mol.: 1 / Mutation: E413A, R422A, R430A
Source method: isolated from a genetically manipulated source
Details: Expressed as AIF(78-613). Residues L614-Q619 remain from Prescission protease cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM1, AIF, PDCD8 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 50 mM NaCl, 24% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32041 / % possible obs: 80.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.37 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 1.152 / Net I/av σ(I): 18.115 / Net I/σ(I): 13.7 / Num. measured all: 200938
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.032.30.3810.801131.6
2.03-2.072.90.360.806138.9
2.07-2.113.60.3120.897143.9
2.11-2.154.20.2860.946149.9
2.15-2.24.70.290.924157.1
2.2-2.255.20.2340.956162.3
2.25-2.315.50.2330.97171.3
2.31-2.375.70.2180.976179.4
2.37-2.446.10.2130.978185
2.44-2.526.30.20.982191.4
2.52-2.616.60.1740.989197.3
2.61-2.7170.1490.9921100
2.71-2.847.30.1370.9921100
2.84-2.997.30.1220.9931100
2.99-3.177.30.1030.9951100
3.17-3.427.10.0880.9961100
3.42-3.767.10.0780.9961100
3.76-4.317.10.0680.9971100
4.31-5.436.90.0650.9971100
5.43-506.20.0670.996199.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å45.16 Å
Translation3 Å45.16 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BV6

4bv6


Resolution: 1.995→45.16 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: ML
Details: Hydrogens were included in riding positions during refinement. FAD cofactor, HEPES, and glycerol geometry restraints were prepared in eLBOW using Mogul (FAD) or simple optimization (HEPES, ...Details: Hydrogens were included in riding positions during refinement. FAD cofactor, HEPES, and glycerol geometry restraints were prepared in eLBOW using Mogul (FAD) or simple optimization (HEPES, glycerol) and included explicitly with the refinement. Residues 78-125, 511-559, and 613-619 are disordered in chains A and B.
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 1590 4.98 %Random selection
Rwork0.1567 ---
obs0.1586 31943 80.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.995→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 74 455 4194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083815
X-RAY DIFFRACTIONf_angle_d0.8765169
X-RAY DIFFRACTIONf_dihedral_angle_d11.5142257
X-RAY DIFFRACTIONf_chiral_restr0.053571
X-RAY DIFFRACTIONf_plane_restr0.005660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9948-2.05920.2193470.21061137X-RAY DIFFRACTION33
2.0592-2.13280.2233800.17461513X-RAY DIFFRACTION45
2.1328-2.21820.1723970.16281909X-RAY DIFFRACTION56
2.2182-2.31920.20631290.15772357X-RAY DIFFRACTION70
2.3192-2.44140.21911500.16562806X-RAY DIFFRACTION83
2.4414-2.59440.2081500.18363238X-RAY DIFFRACTION94
2.5944-2.79470.22431750.18363418X-RAY DIFFRACTION100
2.7947-3.07580.25531940.17333435X-RAY DIFFRACTION100
3.0758-3.52080.1951620.15133460X-RAY DIFFRACTION100
3.5208-4.43520.17111950.13233459X-RAY DIFFRACTION100
4.4352-45.17150.17162110.1513621X-RAY DIFFRACTION99
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)
11.46490.14590.41911.24340.18191.9843-0.04720.2788-0.1128-0.53480.06820.0993-0.00720.0449-0.02410.3808-0.0654-0.050.2271-0.0130.1612-40.010787.4884-0.5301
21.5079-0.3019-0.07291.50630.70691.7953-0.032-0.08930.0149-0.0205-0.08360.5254-0.0419-0.44380.12530.2095-0.0195-0.0170.25140.01710.281-53.915597.082619.7668
30.81020.19220.252.32520.36061.2939-0.09550.00160.0624-0.2430.1981-0.2468-0.2150.2327-0.05340.1679-0.05520.01170.1732-0.00850.1315-29.690799.885117.9235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 402 )
3X-RAY DIFFRACTION3chain 'A' and (resid 403 through 611 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more