[English] 日本語
Yorodumi
- PDB-1ju5: Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ju5
TitleTernary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy
Components
  • (Crk) x 2
  • Abl
KeywordsPROTEIN BINDING/TRANSFERASE / Crk / SH2 / Abl / SH3 / adaptor protein / phosphopeptide / PROTEIN BINDING-TRANSFERASE COMPLEX
Function / homology
Function and homology information


regulation of leukocyte migration / response to hepatocyte growth factor / cellular response to endothelin / regulation of intracellular signal transduction / response to cholecystokinin / helper T cell diapedesis / cerebellar neuron development / regulation of T cell migration / response to peptide / reelin-mediated signaling pathway ...regulation of leukocyte migration / response to hepatocyte growth factor / cellular response to endothelin / regulation of intracellular signal transduction / response to cholecystokinin / helper T cell diapedesis / cerebellar neuron development / regulation of T cell migration / response to peptide / reelin-mediated signaling pathway / protein phosphorylated amino acid binding / mitochondrial depolarization / negative regulation of natural killer cell mediated cytotoxicity / regulation of Rac protein signal transduction / 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 of interleukin-2 production => GO:0032743 / 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 / negative regulation of cell motility / circulatory system development => GO:0072359 / regulation of dendrite development / positive regulation of oxidoreductase activity / activated T cell proliferation / negative regulation of wound healing / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / cellular response to insulin-like growth factor stimulus / regulation of Cdc42 protein signal transduction / signaling adaptor activity / negative regulation of protein serine/threonine kinase activity / regulation of T cell differentiation / negative regulation of ubiquitin-protein transferase activity / signaling receptor complex adaptor activity / regulation of microtubule polymerization / negative regulation of BMP signaling pathway / regulation of actin cytoskeleton reorganization / mitogen-activated protein kinase binding / proline-rich region binding / sequence-specific double-stranded DNA binding / syntaxin binding / cellular response to dopamine / positive regulation of interferon-gamma production => GO:0032729 / negative regulation of cell-cell adhesion / DNA damage induced protein phosphorylation / positive regulation of smooth muscle cell migration / activation of GTPase activity / response to yeast / negative regulation of cellular senescence / positive regulation of osteoblast proliferation / regulation of response to DNA damage stimulus / regulation of protein binding / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / cell leading edge / regulation of signal transduction / negative regulation of long-term synaptic potentiation / actin monomer binding / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / positive regulation of focal adhesion assembly / positive regulation of actin cytoskeleton reorganization / dendrite development / positive regulation of substrate adhesion-dependent cell spreading / mismatch repair / regulation of hematopoietic stem cell differentiation / regulation of cell adhesion mediated by integrin / negative regulation of mitotic cell cycle / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / regulation of cell motility / activation of MAPKK activity / regulation of GTPase activity / endothelial cell migration / four-way junction DNA binding / positive regulation of stress fiber assembly / positive regulation of muscle cell differentiation / cellular response to transforming growth factor beta stimulus / regulation of actin cytoskeleton organization / cellular response to nitric oxide / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading
Protein kinase domain / SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 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 ...Protein kinase domain / SH2 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 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 / CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Tyrosine-protein kinase ABL, SH2 domain / SH3-like domain superfamily / SH2 domain / SH2 domain superfamily / SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Adapter molecule crk / Adapter molecule crk / Tyrosine-protein kinase ABL1
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / ARIA 1.0, CNS 1.0
AuthorsDonaldson, L.W. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide
Authors: Donaldson, L.W. / Gish, G. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Crk
B: Crk
C: Abl


Theoretical massNumber of molelcules
Total (without water)20,3763
Polymers20,3763
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Crk / PROTO-ONCOGENE C-CRK / ADAPTER MOLECULE CRK / P38


Mass: 12142.571 Da / Num. of mol.: 1 / Fragment: Crk SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P46108
#2: Protein/peptide Crk / PROTO-ONCOGENE C-CRK / ADAPTER MOLECULE CRK / P38


Mass: 1468.480 Da / Num. of mol.: 1 / Fragment: Crk phosphopeptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAED4-MMHB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q64010
#3: Protein Abl / proto-oncogene tyrosine-protein kinase


Mass: 6764.461 Da / Num. of mol.: 1 / Fragment: Abl SH3 domain / Mutation: L122K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00519, EC: 2.7.1.112

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D 13C F1-FILTERED F3-EDITED NOESY
141J-HNHA
151IPAP-15N HSQC
NMR detailsText: Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% ...Text: Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% 13C-labeled sample according to Neri et al (Biochemistry 28:7510; 1989). HACAN and CBCA(CO)N(CA)HA experiments were used to assign the proline residues in the Crk SH2 domain according to Kanelis et al (JBNMR 16:253; 2000)

-
Sample preparation

DetailsContents: 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate / pH: 6.8 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian UNITYPLUSVarianUNITYPLUS8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglioprocessing
PIPP4.3.2Garrettdata analysis
CNS1Brungerstructure solution
ARIA1Brungerstructure solution
ARIA1Brungerrefinement
RefinementMethod: ARIA 1.0, CNS 1.0 / Software ordinal: 1
Details: This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2- ...Details: This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2-phosphopeptide intermolecular restraints, 50 hydrogen bonds, 54 direct 3J-HNHA couplings and 166 dihedral angle restraints from TALOS Residues 217-220 and 225-229 of the Crk phosphopeptide (Chain B) are disordered. As intermolecular contacts between the SH2 domain (Chain A) and the SH3 domain (Chain C) limited to amino acids 67-75 in DE-loop of the SH2 domain, there is no unique orientation between the SH2 domain and SH3 domain.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 1

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (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

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