[English] 日本語
Yorodumi
- PDB-1af3: RAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1af3
TitleRAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN
ComponentsAPOPTOSIS REGULATOR BCL-XBcl-2-like protein 1
KeywordsREGULATORY PROTEIN / BCL-XL / APOPTOSIS / MITOCHONDRION / ALTERNATIVE SPLICING
Function / homology
Function and homology information


response to erythropoietin / cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / cellular response to erythropoietin / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / cellular response to prolactin ...response to erythropoietin / cellular response to astaxanthin / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / The NLRP1 inflammasome / cellular response to erythropoietin / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / cellular response to prolactin / BH domain binding / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / 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 / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / cellular response to alkaloid / positive regulation of ATP biosynthetic process / 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 / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to inorganic substance / cellular response to nitric oxide / ectopic germ cell programmed cell death / MDM2/MDM4 family protein binding / cellular response to interleukin-1 / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cAMP / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to organonitrogen compound / response to endoplasmic reticulum stress / mitochondrion organization / cellular response to dexamethasone stimulus / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / response to lead ion / response to virus / cellular response to gamma radiation / response to radiation / response to hydrogen peroxide / synaptic vesicle membrane / response to organic cyclic compound / cerebral cortex development / response to peptide hormone / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to xenobiotic stimulus / presynapse / GTPase binding / cellular response to tumor necrosis factor / cellular response to hypoxia / spermatogenesis / neuron apoptotic process / regulation of apoptotic process / nuclear membrane / mitochondrial inner membrane / response to oxidative stress / negative regulation of neuron apoptotic process / in utero embryonic development / mitochondrial outer membrane / response to lipopolysaccharide / response to hypoxia / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / centrosome / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity
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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsAritomi, M. / Kunishima, N. / Inohara, N. / Ishibashi, Y. / Ohta, S. / Morikawa, K.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of rat Bcl-xL. Implications for the function of the Bcl-2 protein family.
Authors: Aritomi, M. / Kunishima, N. / Inohara, N. / Ishibashi, Y. / Ohta, S. / Morikawa, K.
History
DepositionMar 21, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APOPTOSIS REGULATOR BCL-X


Theoretical massNumber of molelcules
Total (without water)22,0821
Polymers22,0821
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.050, 64.050, 112.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein APOPTOSIS REGULATOR BCL-X / Bcl-2-like protein 1


Mass: 22082.246 Da / Num. of mol.: 1 / Fragment: SOLUBLE REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P53563
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlBcl-Xl(B)1drop
250 mMMES1drop
35 %(v/v)glycerol1drop
41 mMdithiothreitol1drop
5100 mM1dropNaCl
60.7 Mammonium sulfate1drop
7100 mMMES1reservoir
810 %(v/v)glycerol1reservoir
92 mMdithiothreitol1reservoir
101.4 M1reservoirNa2SO4

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8614 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 2 / Rsym value: 0.962 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 68982

-
Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 560 6.5 %RANDOM
Rwork0.222 ---
obs0.225 8564 99 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 0 51 1227
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 8564
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg2.66

+
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