[English] 日本語
Yorodumi
- PDB-1zy3: Structural model of complex of Bcl-w protein with Bid BH3-peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zy3
TitleStructural model of complex of Bcl-w protein with Bid BH3-peptide
Components
  • Apoptosis regulator Bcl-W
  • BH3-peptide from BH3 interacting domain death agonist protein
KeywordsAPOPTOSIS / Bcl-w / BH3-peptide
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Sertoli cell proliferation / Activation, myristolyation of BID and translocation to mitochondria / BH domain binding / positive regulation of fibroblast apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members ...negative regulation of mitochondrial membrane permeability / cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Sertoli cell proliferation / Activation, myristolyation of BID and translocation to mitochondria / BH domain binding / positive regulation of fibroblast apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / Bcl-2 family protein complex / regulation of T cell proliferation / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / regulation of G1/S transition of mitotic cell cycle / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / mitochondrial ATP synthesis coupled electron transport / cellular response to glycine / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / signal transduction in response to DNA damage / supramolecular fiber organization / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / cellular response to estradiol stimulus / response to ischemia / positive regulation of protein-containing complex assembly / cellular response to amyloid-beta / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / spermatogenesis / protein-containing complex assembly / regulation of apoptotic process / neuron apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / identical protein binding / membrane / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-W / BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like ...Apoptosis regulator, Bcl-W / BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BH3-interacting domain death agonist / Bcl-2-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Rigid body docking, semi-flexible simulated annealing, refinement using explicit water
AuthorsDenisov, A.Y. / Gehring, K.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Model of the BCL-w-BID Peptide Complex and Its Interactions with Phospholipid Micelles.
Authors: Denisov, A.Y. / Chen, G. / Sprules, T. / Moldoveanu, T. / Beauparlant, P. / Gehring, K.
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 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 Bcl-W
B: BH3-peptide from BH3 interacting domain death agonist protein


Theoretical massNumber of molelcules
Total (without water)21,9022
Polymers21,9022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Apoptosis regulator Bcl-W / Bcl-2-like 2 protein


Mass: 19659.885 Da / Num. of mol.: 1 / Fragment: residues 2-171 / Mutation: P116V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-29b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92843
#2: Protein/peptide BH3-peptide from BH3 interacting domain death agonist protein / BID


Mass: 2241.615 Da / Num. of mol.: 1 / Mutation: R203K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55957

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCA(CO)HN
13215N-edited NOESY
142HNHA
15315N-edited NOESY
16315N-1H HSQC
NMR detailsText: This model structure was obtained using ambigous chemical shift perturbation constraints, NOE distances and hydrogen bonds

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM Bcl-w U-15N,13C, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
20.7 mM Bcl-w U-15N, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
30.7 mM Bid BH3-peptide U-15N, 0.7 mM Bcl-w, 20 mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM NaCl / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUnity Inova8001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.2Bonvin et al.refinement
NMRPipe2Delargio et al.processing
XEASY1.3.13Bartels et al.data analysis
HADDOCK1.2Bonvin et al.processing
RefinementMethod: Rigid body docking, semi-flexible simulated annealing, refinement using explicit water
Software ordinal: 1
Details: 200 conformers were obtained in the rigid body docking and 100 best conformers were selected for semi-flexible simulated annealing following by refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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://pdbjlvh1.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