[English] 日本語
Yorodumi
- PDB-5miu: G307E variant of Murine Apoptosis Inducing Factor (oxidized state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5miu
TitleG307E variant of Murine Apoptosis Inducing Factor (oxidized state)
ComponentsApoptosis-inducing factor 1, mitochondrial
KeywordsOXIDOREDUCTASE / Apoptosis Inducing Factor OXIDOREDUCTASE
Function / homology
Function and homology information


electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / protein import into the intermembrane space via the disulfide relay system / 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 / apoptotic mitochondrial changes ...electron-transferring-flavoprotein dehydrogenase activity / regulation of apoptotic DNA fragmentation / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / protein import into the intermembrane space via the disulfide relay system / 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 / apoptotic mitochondrial changes / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / FAD binding / mitochondrial intermembrane space / neuron differentiation / positive regulation of neuron apoptotic process / neuron apoptotic process / response to oxidative stress / mitochondrial outer membrane / protein dimerization activity / mitochondrial inner membrane / 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 / : / 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 / Apoptosis-inducing factor 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSorrentino, L. / Cossu, F. / Milani, M. / Aliverti, A. / 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
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
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3724
Polymers116,8012
Non-polymers1,5712
Water45025
1
A: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1862
Polymers58,4001
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis-inducing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1862
Polymers58,4001
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.040, 110.060, 119.590
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: 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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000,0.2 M sodium acetate, pH 8.5

-
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: 3.5→48.7 Å / Num. obs: 16448 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.973 / Rrim(I) all: 0.0393 / Net I/σ(I): 5.3
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1197 / CC1/2: 0.735 / Rrim(I) all: 0.1295 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD3

3gd3


Resolution: 3.5→48.7 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27857 857 5.2 %RANDOM
Rwork0.21175 ---
obs0.21524 15590 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.943 Å2
Baniso -1Baniso -2Baniso -3
1--6.89 Å20 Å20 Å2
2---3.48 Å20 Å2
3---10.37 Å2
Refinement stepCycle: 1 / Resolution: 3.5→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 106 25 7086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197209
X-RAY DIFFRACTIONr_bond_other_d00.026988
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9779760
X-RAY DIFFRACTIONr_angle_other_deg3.639316056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85123.592309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.818151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4591555
X-RAY DIFFRACTIONr_chiral_restr0.0830.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218094
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021639
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_it3.2137.1723595
X-RAY DIFFRACTIONr_mcbond_other3.2127.1723594
X-RAY DIFFRACTIONr_mcangle_it5.3910.754485
X-RAY DIFFRACTIONr_mcangle_other5.3910.7494486
X-RAY DIFFRACTIONr_scbond_it3.4867.4153614
X-RAY DIFFRACTIONr_scbond_other3.4857.4153615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.83510.9865276
X-RAY DIFFRACTIONr_long_range_B_refined8.84456.0717853
X-RAY DIFFRACTIONr_long_range_B_other8.84456.0737854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 78 -
Rwork0.347 1111 -
obs--99.66 %

+
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