[English] 日本語
Yorodumi
- PDB-2k7w: BAX Activation is Initiated at a Novel Interaction Site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k7w
TitleBAX Activation is Initiated at a Novel Interaction Site
Components
  • Apoptosis regulator BAX
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / BAX / BIM / BH3 / BCL-2
Function / homology
Function and homology information


positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / BIM-BCL-xl complex ...positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of apoptotic DNA fragmentation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / apoptotic process involved in mammary gland involution / apoptotic process involved in embryonic digit morphogenesis / B cell negative selection / BAK complex / positive regulation of fibroblast apoptotic process / retinal cell programmed cell death / glycosphingolipid metabolic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / Activation of BIM and translocation to mitochondria / developmental pigmentation / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / ear development / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of apoptotic process involved in mammary gland involution / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / regulation of nitrogen utilization / regulation of organ growth / positive regulation of T cell apoptotic process / tube formation / mammary gland development / endoplasmic reticulum calcium ion homeostasis / fertilization / meiosis I / epithelial cell apoptotic process / motor neuron apoptotic process / calcium ion transport into cytosol / positive regulation of epithelial cell apoptotic process / mitochondrial fusion / myeloid cell homeostasis / Bcl-2 family protein complex / execution phase of apoptosis / cellular response to glucocorticoid stimulus / odontogenesis of dentin-containing tooth / NRAGE signals death through JNK / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / B cell homeostasis / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / pore complex / apoptotic mitochondrial changes / T cell homeostasis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / vagina development / germ cell development / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / negative regulation of apoptotic signaling pathway / cellular response to unfolded protein / positive regulation of calcium ion transport into cytosol / Pyroptosis / response to axon injury / blood vessel remodeling / negative regulation of protein binding / spleen development / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / release of sequestered calcium ion into cytosol / positive regulation of intrinsic apoptotic signaling pathway / response to salt stress / supramolecular fiber organization
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
Bcl-2-like protein 11 / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGavathiotis, E. / Suzuki, M. / Davis, M.L. / Pitter, K. / Bird, G.H. / Katz, S.G. / Tu, H.C. / Kim, H. / Cheng, E.H. / Tjandra, N. / Walensky, L.D.
CitationJournal: Nature / Year: 2008
Title: BAX activation is initiated at a novel interaction site.
Authors: Gavathiotis, E. / Suzuki, M. / Davis, M.L. / Pitter, K. / Bird, G.H. / Katz, S.G. / Tu, H.C. / Kim, H. / Cheng, E.H. / Tjandra, N. / Walensky, L.D.
History
DepositionAug 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)23,6642
Polymers23,6642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1500structures with the lowest energy
RepresentativeModel #1

-
Components

#1: Protein Apoptosis regulator BAX


Mass: 21204.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-interacting mediator of cell death


Mass: 2459.711 Da / Num. of mol.: 1 / Fragment: BIM BH3 domain / Source method: obtained synthetically / References: UniProt: O43521

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC
NMR detailsText: BAX-BIM SAHB INTERACTION ANALYSIS, PARAMAGNETIC SPIN-LABELING NMR

-
Sample preparation

DetailsContents: 0.1-0.2 mM [U-99% 15N] protein, 0.1-0.2 mM peptide, 90% H2O/10%D20
Solvent system: 90% H2O/10%D20
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein[U-99% 15N]0.1-0.21
mMpeptide0.1-0.21
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, B. et al.data analysis
CNSBrunger, A. et al.refinement
NMRPipeDelaglio, F. et al.processing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: STRUCTURES CALCULATED WITH HADDOCK 2.0
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1500 / Conformers submitted total number: 20

+
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