|Entry||Database: PDB / ID: 2abl|
|Title||SH3-SH2 DOMAIN FRAGMENT OF HUMAN BCR-ABL TYROSINE KINASE|
|Components||ABL TYROSINE KINASE|
|Keywords||TRANSFERASE / TYROSINE KINASE / SH3 / SH2 / ONCOPROTEIN|
|Function / homology|
Function and homology information
mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity ...mitochondrial depolarization / positive regulation of interleukin-2 production => GO:0032743 / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / alpha-beta T cell differentiation / B cell proliferation involved in immune response / regulation of modification of synaptic structure / positive regulation of microtubule binding / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / neuroepithelial cell differentiation / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / actin filament branching / positive regulation of oxidoreductase activity / activated T cell proliferation / circulatory system development => GO:0072359 / neuropilin binding / neuropilin signaling pathway / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / regulation of T cell differentiation / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / negative regulation of BMP signaling pathway / regulation of actin cytoskeleton reorganization / mitogen-activated protein kinase binding / positive regulation of interferon-gamma production => GO:0032729 / proline-rich region binding / syntaxin binding / cellular response to dopamine / DNA damage induced protein phosphorylation / negative regulation of cell-cell adhesion / positive regulation of osteoblast proliferation / negative regulation of cellular senescence / regulation of response to DNA damage stimulus / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / cell leading edge / negative regulation of long-term synaptic potentiation / actin monomer binding / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / regulation of endocytosis / positive regulation of actin cytoskeleton reorganization / mismatch repair / regulation of hematopoietic stem cell differentiation / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / regulation of cell motility / negative regulation of mitotic cell cycle / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of muscle cell differentiation / positive regulation of stress fiber assembly / four-way junction DNA binding / signal transduction in response to DNA damage / regulation of actin cytoskeleton organization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / sequence-specific double-stranded DNA binding / regulation of autophagy / cellular protein modification process / spleen development / negative regulation of I-kappaB kinase/NF-kappaB signaling / post-embryonic development / positive regulation of mitotic cell cycle / positive regulation of release of sequestered calcium ion into cytosol / SH2 domain binding / negative regulation of ERK1 and ERK2 cascade / thymus development / phosphotyrosine residue binding / protein kinase C binding / neural tube closure / ephrin receptor binding / integrin-mediated signaling pathway / peptidyl-tyrosine autophosphorylation / actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / establishment of protein localization / SH3 domain binding / autophagy / postsynapse / cell cycle arrest / epidermal growth factor receptor signaling pathway / cellular response to hydrogen peroxide / positive regulation of neuron death / B cell receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis
SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinase domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl ...SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinase domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / SH3 domain / SH2 domain / SH3-like domain superfamily / SH3 domain / SH2 domain superfamily / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Tyrosine-protein kinase ABL1
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å|
|Authors||Nam, H.-J. / Frederick, C.A.|
|Citation||Journal: Structure / Year: 1996|
Title: Intramolecular interactions of the regulatory domains of the Bcr-Abl kinase reveal a novel control mechanism.
Authors: Nam, H.J. / Haser, W.G. / Roberts, T.M. / Frederick, C.A.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: ABL TYROSINE KINASE
|#1: Protein|| |
Mass: 18122.951 Da / Num. of mol.: 1 / Fragment: SH3-SH2 DOMAIN FRAGMENT / Mutation: INS(M76)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: ABL SH3-SH2 / Plasmid: PRSET / Species (production host): Escherichia coli / Gene (production host): ABL SH3-SH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00519, EC: 188.8.131.52
|#2: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.25 Å3/Da / Density % sol: 45.32 %|
|Crystal grow||pH: 7.5 / Details: pH 7.5|
*PLUSMethod: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of mother liquor
|Components of the solutions|
|Diffraction||Mean temperature: 293 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418|
|Detector||Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRRORS|
|Radiation||Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 2.5→12 Å / Num. obs: 5585 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rsym value: 0.048|
|Reflection shell||Resolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rsym value: 0.14 / % possible all: 98|
*PLUSNum. measured all: 19460 / Rmerge(I) obs: 0.048
*PLUS% possible obs: 98 % / Rmerge(I) obs: 0.14
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: ABL SH3, SRC SH2
Resolution: 2.5→10 Å / Cross valid method: FREE-R / σ(F): 2
|Refinement step||Cycle: LAST / Resolution: 2.5→10 Å|
|Refine LS restraints|
*PLUSName: X-PLOR / Version: 3 / Classification: refinement
|Refine LS restraints|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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
+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.
+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
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