[English] 日本語
Yorodumi
- PDB-5w62: Crystal structure of mouse BAX monomer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w62
TitleCrystal structure of mouse BAX monomer
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / monomer / mouse
Function / homology
Function and homology information


Activation, translocation and oligomerization of BAX / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane ...Activation, translocation and oligomerization of BAX / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of animal secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / glycosphingolipid metabolic process / retinal cell programmed cell death / B cell negative selection / BAK complex / BH domain binding / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / sex differentiation / mitochondrial fragmentation involved in apoptotic process / post-embryonic camera-type eye morphogenesis / apoptotic process involved in blood vessel morphogenesis / limb morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / fertilization / regulation of mitochondrial membrane permeability involved in apoptotic process / Bcl-2 family protein complex / mitochondrial fusion / myeloid cell homeostasis / execution phase of apoptosis / thymocyte apoptotic process / response to ionizing radiation / hypothalamus development / pore complex / odontogenesis of dentin-containing tooth / germ cell development / vagina development / B cell homeostasis / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of apoptotic signaling pathway / homeostasis of number of cells / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of calcium ion transport into cytosol / blood vessel remodeling / ectopic germ cell programmed cell death / response to axon injury / ovarian follicle development / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / supramolecular fiber organization / heat shock protein binding / homeostasis of number of cells within a tissue / intrinsic apoptotic signaling pathway / Hsp70 protein binding / release of cytochrome c from mitochondria / regulation of neuron apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / response to gamma radiation / post-embryonic development / regulation of mitochondrial membrane potential / kidney development / mitochondrion organization / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to virus / cerebral cortex development / response to wounding / male gonad development / mitochondrial membrane / response to toxic substance / intrinsic apoptotic signaling pathway in response to DNA damage / neuron migration / cellular response to UV / nuclear envelope / nervous system development / positive regulation of neuron apoptotic process / protein-folding chaperone binding / channel activity
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator BAX
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsRobin, A.Y. / Colman, P.M. / Czabotar, P.E. / Luo, C.S.
CitationJournal: Structure / Year: 2018
Title: Ensemble Properties of Bax Determine Its Function.
Authors: Robin, A.Y. / Iyer, S. / Birkinshaw, R.W. / Sandow, J. / Wardak, A. / Luo, C.S. / Shi, M. / Webb, A.I. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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 regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4772
Polymers21,3811
Non-polymers961
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.787, 51.950, 62.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Apoptosis regulator BAX


Mass: 21381.400 Da / Num. of mol.: 1 / Mutation: C62S C126S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bax / Production host: Escherichia coli (E. coli) / References: UniProt: Q07813
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.56 Å3/Da / Density % sol: 21.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, TRIS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.196→34.236 Å / Num. obs: 7218 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0685 / Net I/σ(I): 18.44
Reflection shellHighest resolution: 2.196 Å / Rmerge(I) obs: 0.9765 / CC1/2: 0.695

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BD2, 5W60

4bd2

5w60


Resolution: 2.196→34.236 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.2842 722 10 %
Rwork0.2082 --
obs0.216 7218 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.196→34.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 5 26 1237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061236
X-RAY DIFFRACTIONf_angle_d0.7471677
X-RAY DIFFRACTIONf_dihedral_angle_d10.999710
X-RAY DIFFRACTIONf_chiral_restr0.043193
X-RAY DIFFRACTIONf_plane_restr0.005206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1962-2.36570.31941410.24591268X-RAY DIFFRACTION100
2.3657-2.60370.33021420.24141274X-RAY DIFFRACTION100
2.6037-2.98030.32671400.2351272X-RAY DIFFRACTION100
2.9803-3.75410.31331450.20581310X-RAY DIFFRACTION100
3.7541-34.23980.24741540.19121372X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.1366 Å / Origin y: -0.6044 Å / Origin z: -13.1954 Å
111213212223313233
T0.2872 Å2-0.0409 Å2-0.0306 Å2-0.273 Å2-0.0087 Å2--0.2873 Å2
L1.7039 °2-0.8979 °20.2803 °2-2.6925 °2-1.6853 °2--2.8669 °2
S0.1709 Å °-0.0931 Å °0.0295 Å °-0.143 Å °0.0827 Å °0.1795 Å °0.1424 Å °0.0008 Å °0.0044 Å °
Refinement TLS groupSelection details: chain 'A'

+
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