[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


MET activates RAP1 and RAC1 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / Myogenesis / VEGFA-VEGFR2 Pathway / Role of ABL in ROBO-SLIT signaling / p130Cas linkage to MAPK signaling for integrins ...MET activates RAP1 and RAC1 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / Myogenesis / VEGFA-VEGFR2 Pathway / Role of ABL in ROBO-SLIT signaling / p130Cas linkage to MAPK signaling for integrins / Regulation of actin dynamics for phagocytic cup formation / Downstream signal transduction / ARMS-mediated activation / MET receptor recycling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX2 regulates osteoblast differentiation / Regulation of signaling by CBL / Regulation of signaling by CBL / MET receptor recycling / MET activates RAP1 and RAC1 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / VEGFA-VEGFR2 Pathway / p130Cas linkage to MAPK signaling for integrins / Regulation of actin dynamics for phagocytic cup formation / Downstream signal transduction / ARMS-mediated activation / Factors involved in megakaryocyte development and platelet production / regulation of leukocyte migration / response to peptide / response to hepatocyte growth factor / cellular response to endothelin / response to cholecystokinin / helper T cell diapedesis / protein phosphorylated amino acid binding / cerebellar neuron development / regulation of T cell migration / reelin-mediated signaling pathway / mitochondrial depolarization / regulation of Rac protein signal transduction / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of actin filament binding / transitional one stage B cell differentiation / 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 / positive regulation of Wnt signaling pathway, planar cell polarity pathway / neuroepithelial cell differentiation / regulation of extracellular matrix organization / microspike assembly / cerebellum morphogenesis / regulation of modification of synaptic structure / regulation of dendrite development / collateral sprouting / negative regulation of wound healing / negative regulation of cell motility / B-1 B cell homeostasis / cardiovascular system development / positive regulation of oxidoreductase activity / alpha-beta T cell differentiation / activated T cell proliferation / bubble DNA binding / neuropilin signaling pathway / neuropilin binding / regulation of T cell differentiation / regulation of Cdc42 protein signal transduction / cellular response to insulin-like growth factor stimulus / 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 / activation of GTPase activity / regulation of response to DNA damage stimulus / regulation of protein binding / response to yeast / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of osteoblast proliferation / cell leading edge / regulation of axon extension / SH3/SH2 adaptor activity / 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
Src homology 2 (SH2) domain profile. / SH2 domain / CRK, C-terminal SH3 domain / Tyrosine-protein kinase ABL, SH2 domain / SH3-like domain superfamily / SH2 domain superfamily / Tyrosine protein kinases specific active-site signature. / Protein kinase domain profile. / SH3 domain / Variant SH3 domain ...Src homology 2 (SH2) domain profile. / SH2 domain / CRK, C-terminal SH3 domain / Tyrosine-protein kinase ABL, SH2 domain / SH3-like domain superfamily / SH2 domain superfamily / Tyrosine protein kinases specific active-site signature. / Protein kinase domain profile. / SH3 domain / Variant SH3 domain / Protein tyrosine kinase / F-actin binding / Protein kinases ATP-binding region signature. / 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 / Src homology 3 (SH3) domain profile.
Tyrosine-protein kinase ABL1 / Adapter molecule crk / Adapter molecule crk
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/peptide 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/peptide 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-ID: 1 / Solution-ID: 1

Experiment-IDType
13D 13C-separated NOESY
23D 15N-separated NOESY
33D 13C F1-FILTERED F3-EDITED NOESY
4J-HNHA
5IPAP-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% 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

Manufacturer: Varian / Model: UNITYPLUS / Type: Varian UNITYPLUS

Field strength (MHz)Spectrometer-ID
5001
6002
8003

-
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-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

-
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