[English] 日本語
Yorodumi
- PDB-1m6i: Crystal Structure of Apoptosis Inducing Factor (AIF) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m6i
TitleCrystal Structure of Apoptosis Inducing Factor (AIF)
ComponentsProgrammed cell death protein 8
KeywordsOXIDOREDUCTASE / Apoptosis / AIF
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 / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / positive regulation of necroptotic process / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate ...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 / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / positive regulation of necroptotic process / oxidoreductase activity, acting on NAD(P)H / response to L-glutamate / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / FAD binding / 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 / protein dimerization activity / mitochondrial inner membrane / 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 ...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 / SOLVE / Resolution: 1.8 Å
AuthorsYe, H. / Cande, C. / Stephanou, N.C. / Jiang, S. / Gurbuxani, S. / Larochette, N. / Daugas, E. / Garrido, C. / Kroemer, G. / Wu, H.
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
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7302
Polymers53,9441
Non-polymers7861
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.9, 90.5, 60.5
Angle α, β, γ (deg.)90, 94.6, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Programmed cell death protein 8 / Apoptosis-Inducing factor


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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95831
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG8000, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein11
216 %(w/v)PEG800012
35 mMdithiothreitol12
4100 mMTris12pH8.0

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9997 Å
DetectorDetector: CCD / Date: Sep 24, 2001 / Details: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 1.8→30.16 Å / Num. obs: 44620 / Observed criterion σ(I): 2
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.264

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: SOLVE / Resolution: 1.8→30.16 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 2700 -Random
Rwork0.2253 ---
all-50709 --
obs-44620 93.4 %-
Displacement parametersBiso mean: -1.123 Å2
Baniso -1Baniso -2Baniso -3
1--2.479 Å20 Å20.761 Å2
2---0.654 Å20 Å2
3---3.133 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 53 235 3814
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3

+
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