[English] 日本語
Yorodumi
- PDB-1ab2: THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRC HOMOLOGY 2 DOMAIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ab2
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRC HOMOLOGY 2 DOMAIN OF C-ABL
ComponentsC-ABL TYROSINE KINASE SH2 DOMAIN
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / RUNX2 regulates osteoblast differentiation / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs ...Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / RUNX2 regulates osteoblast differentiation / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / mitochondrial depolarization / transitional one stage B cell differentiation / positive regulation of actin filament binding / DNA conformation change / activation of protein kinase C activity / negative regulation of phospholipase C activity / actin filament branching / positive regulation of interleukin-2 secretion / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / B cell proliferation involved in immune response / positive regulation of microtubule binding / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / microspike assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / cardiovascular system development / alpha-beta T cell differentiation / positive regulation of oxidoreductase activity / activated T cell proliferation / bubble DNA binding / neuropilin signaling pathway / neuropilin binding / regulation of T cell differentiation / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / regulation of actin cytoskeleton reorganization / negative regulation of BMP signaling pathway / mitogen-activated protein kinase binding / sequence-specific double-stranded DNA binding / proline-rich region binding / positive regulation of interferon-gamma secretion / negative regulation of cell-cell adhesion / cellular response to dopamine / syntaxin binding / regulation of response to DNA damage stimulus / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / positive regulation of osteoblast proliferation / cell leading edge / regulation of axon extension / actin monomer binding / positive regulation of cell migration involved in sprouting angiogenesis / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / Bergmann glial cell differentiation / mismatch repair / regulation of hematopoietic stem cell differentiation / positive regulation of focal adhesion assembly / positive regulation of muscle cell differentiation / positive regulation of actin cytoskeleton reorganization / regulation of endocytosis / regulation of cell adhesion / negative regulation of mitotic cell cycle / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell motility / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / endothelial cell migration / positive regulation of stress fiber assembly / regulation of actin cytoskeleton organization / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading / regulation of autophagy / positive regulation of endothelial cell migration / cellular protein modification process / spleen development / SH2 domain binding / post-embryonic development / neural tube closure / positive regulation of mitotic cell cycle / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / negative regulation of ERK1 and ERK2 cascade / phosphotyrosine residue binding / ephrin receptor binding / integrin-mediated signaling pathway / actin cytoskeleton organization / autophagy / non-specific protein-tyrosine kinase / peptidyl-tyrosine autophosphorylation
Tyrosine-protein kinase ABL1/transforming protein Abl / Protein tyrosine kinase / Protein kinase, ATP binding site / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinases ATP-binding region signature. / F-actin binding / SH3 domain ...Tyrosine-protein kinase ABL1/transforming protein Abl / Protein tyrosine kinase / Protein kinase, ATP binding site / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinases ATP-binding region signature. / F-actin binding / SH3 domain / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Tyrosine-protein kinase ABL, SH2 domain / Protein kinase-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Protein kinase domain / Protein kinase domain profile. / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain / SH3 domain / F-actin binding
Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsOverduin, M. / Rios, C.B. / Mayer, B.J. / Baltimore, D. / Cowburn, D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: Three-dimensional solution structure of the src homology 2 domain of c-abl.
Authors: Overduin, M. / Rios, C.B. / Mayer, B.J. / Baltimore, D. / Cowburn, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Secondary Structure of Src Homology 2 Domain of C-Abl by Heteronuclear NMR Spectroscopy in Solution
Authors: Overduin, M. / Mayer, B. / Rios, C.B. / Baltimore, D. / Cowburn, D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 19, 1993-
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-ABL TYROSINE KINASE SH2 DOMAIN


Theoretical massNumber of molelcules
Total (without water)12,1591
Polymers12,1591
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein/peptide C-ABL TYROSINE KINASE SH2 DOMAIN


Mass: 12159.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00519, EC: 2.7.1.112

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR ensembleConformers submitted total number: 20

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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