[English] 日本語
Yorodumi
- PDB-1bxl: STRUCTURE OF BCL-XL/BAK PEPTIDE COMPLEX, NMR, MINIMIZED AVERAGE S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bxl
TitleSTRUCTURE OF BCL-XL/BAK PEPTIDE COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • BAK PEPTIDE
  • BCL-XL
KeywordsCOMPLEX (APOPTOSIS/PEPTIDE) / APOPTOSIS / ALTERNATIVE SPLICING / COMPLEX (APOPTOSIS-PEPTIDE) / COMPLEX (APOPTOSIS-PEPTIDE) complex
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis / apoptotic process in bone marrow cell / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / establishment or maintenance of transmembrane electrochemical gradient / dendritic cell proliferation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / myeloid cell homeostasis / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / positive regulation of calcium ion transport into cytosol / response to cycloheximide / porin activity / cellular response to alkaloid / thymocyte apoptotic process / STAT5 activation downstream of FLT3 ITD mutants / pore complex / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / animal organ regeneration / Pyroptosis / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of peptidyl-serine phosphorylation / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / apoptotic signaling pathway / establishment of localization in cell / positive regulation of protein-containing complex assembly / response to gamma radiation / cellular response to amino acid stimulus / response to hydrogen peroxide / cellular response to gamma radiation / synaptic vesicle membrane / response to organic cyclic compound / endocytosis / cellular response to mechanical stimulus / RAS processing / male gonad development / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / spermatogenesis / defense response to virus / neuron apoptotic process
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / 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-X / Apoptosis regulator, Bcl-2/ BclX / 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
Bcl-2-like protein 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsSattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H. / Shuker, S.B. / Chang, B.S. / Minn, A.J. ...Sattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H. / Shuker, S.B. / Chang, B.S. / Minn, A.J. / Thompson, C.B. / Fesik, S.W.
CitationJournal: Science / Year: 1997
Title: Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis.
Authors: Sattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H.S. / Shuker, S.B. / Chang, B.S. / Minn, A.J. / Thompson, C.B. / Fesik, S.W.
History
DepositionOct 16, 1996Processing site: BNL
Revision 1.0Oct 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-XL
B: BAK PEPTIDE


Theoretical massNumber of molelcules
Total (without water)26,6062
Polymers26,6062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein BCL-XL /


Mass: 24879.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HMS174 (DE3) / Plasmid: PET29B
Gene (production host): HUMAN BCL-XL, RESIDUES 1-44, 85-205, DELETION MUTANT LACKING A FLEXIBLE LOOP (RESIDUES 45-84) AND THE C-TERMINAL HYDROPHOBIC REGION, WITH A C-TERMINAL HIS-TAG
Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide BAK PEPTIDE


Mass: 1726.934 Da / Num. of mol.: 1 / Fragment: RESIDUES 572 - 587 OF BAK PROTEIN
Source method: isolated from a genetically manipulated source
References: UniProt: Q16611

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NMR SPECTRA WERE RECORDED ON 1-3 MM SOLUTIONS OF BCL-XL COMPLEXED WITH A BAK PEPTIDE IN 10 MM SODIUM PHOSPHATE BUFFER (PH 6.5) AT 303K.

-
Sample preparation

Sample conditionsTemperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

+
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