[English] 日本語
Yorodumi
- PDB-1g5m: HUMAN BCL-2, ISOFORM 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g5m
TitleHUMAN BCL-2, ISOFORM 1
ComponentsPROTEIN (APOPTOSIS REGULATOR BCL-2 WITH PUTATIVE FLEXIBLE LOOP REPLACED WITH A PORTION OF APOPTOSIS REGULATOR BCL-X PROTEIN)
KeywordsAPOPTOSIS
Function / homology
Function and homology information


: / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / positive regulation of neuron maturation ...: / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / positive regulation of neuron maturation / channel inhibitor activity / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / apoptotic process in bone marrow cell / dendritic cell apoptotic process / renal system process / regulation of cell-matrix adhesion / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / The NLRP1 inflammasome / ear development / negative regulation of calcium ion transport into cytosol / SARS-CoV-1-mediated effects on programmed cell death / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / regulation of nitrogen utilization / glomerulus development / regulation of transmembrane transporter activity / focal adhesion assembly / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / B cell apoptotic process / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of multicellular organism growth / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / negative regulation of execution phase of apoptosis / calcium ion transport into cytosol / oocyte development / fertilization / regulation of growth / negative regulation of ossification / response to UV-B / response to iron ion / epithelial cell apoptotic process / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / axon regeneration / motor neuron apoptotic process / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of smooth muscle cell migration / negative regulation of B cell apoptotic process / organ growth / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / digestive tract morphogenesis / B cell lineage commitment / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / hepatocyte apoptotic process / pore complex / regulation of calcium ion transport / germ cell development / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / T cell homeostasis / B cell homeostasis / apoptotic mitochondrial changes / humoral immune response / B cell proliferation / negative regulation of anoikis / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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-2 / 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-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 Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPetros, A.M. / Medek, A. / Nettesheim, D.G. / Kim, D.H. / Yoon, H.S. / Swift, K. / Matayoshi, E.D. / Oltersdorf, T. / Fesik, S.W.
Citation
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Analysis of the structure, transcripts, and products of bcl-2, the gene involved in human follicular lymphoma
Authors: Tsujimoto, Y. / Croce, C.M.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (APOPTOSIS REGULATOR BCL-2 WITH PUTATIVE FLEXIBLE LOOP REPLACED WITH A PORTION OF APOPTOSIS REGULATOR BCL-X PROTEIN)


Theoretical massNumber of molelcules
Total (without water)19,2271
Polymers19,2271
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)1 / -
Representative

-
Components

#1: Protein PROTEIN (APOPTOSIS REGULATOR BCL-2 WITH PUTATIVE FLEXIBLE LOOP REPLACED WITH A PORTION OF APOPTOSIS REGULATOR BCL-X PROTEIN)


Mass: 19227.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10415, UniProt: Q07817

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
115N-Bcl-2(1); 15N,13C-BCL-2(1)H2O
215N,13C-Bcl-2(1)D2O
Sample conditionsIonic strength: 20 mM / pH: 7.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

-
Processing

NMR softwareName: CNX / Version: 2000 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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