[English] 日本語
Yorodumi
- PDB-1jeg: Solution structure of the SH3 domain from C-terminal Src Kinase c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jeg
TitleSolution structure of the SH3 domain from C-terminal Src Kinase complexed with a peptide from the tyrosine phosphatase PEP
Components
  • HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP
  • TYROSINE-PROTEIN KINASE CSK
KeywordsTRANSFERASE/HYDROLASE / SH3 domain / protein-peptide complex / tyrosine phosphatase / kinase / TRANSFERASE-HYDROLASE COMPLEX
Function / homology
Function and homology information


positive regulation of granzyme B production / phosphoanandamide dephosphorylation / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Negative regulation of FLT3 / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...positive regulation of granzyme B production / phosphoanandamide dephosphorylation / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Negative regulation of FLT3 / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Co-inhibition by PD-1 / regulation of natural killer cell proliferation / positive regulation of toll-like receptor 3 signaling pathway / regulation of leukocyte migration / positive regulation of toll-like receptor 7 signaling pathway / Integrin signaling / positive regulation of toll-like receptor 9 signaling pathway / MAP2K and MAPK activation / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of T cell activation / negative regulation of interleukin-8 production / adherens junction organization / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / protein kinase A catalytic subunit binding / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of interleukin-6 production / oligodendrocyte differentiation / positive regulation of interferon-alpha production / T cell differentiation / negative regulation of tumor necrosis factor production / protein dephosphorylation / positive regulation of defense response to virus by host / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / positive regulation of protein import into nucleus / lipid metabolic process / autophagy / kinase binding / cytoplasmic side of plasma membrane / cell-cell junction / T cell receptor signaling pathway / transferase activity / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / perinuclear region of cytoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Non-receptor tyrosine-protein phosphatase 22 / : / CSK-like, SH2 domain / : / SH3 Domains / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / : ...Non-receptor tyrosine-protein phosphatase 22 / : / CSK-like, SH2 domain / : / SH3 Domains / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / : / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 22 / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsional angle dynmaics
AuthorsGhose, R. / Shekhtman, A. / Goger, M.J. / Ji, H. / Cowburn, D.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: A novel, specific interaction involving the Csk SH3 domain and its natural ligand.
Authors: Ghose, R. / Shekhtman, A. / Goger, M.J. / Ji, H. / Cowburn, D.
History
DepositionJun 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE CSK
B: HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP


Theoretical massNumber of molelcules
Total (without water)12,1112
Polymers12,1112
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)25 / 1000structures with the lowest energy
Representative

-
Components

#1: Protein TYROSINE-PROTEIN KINASE CSK / C-SRC KINASE / PROTEIN-TYROSINE KINASE CYL


Mass: 9198.627 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P41241, EC: 2.7.1.112
#2: Protein/peptide HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP


Mass: 2912.187 Da / Num. of mol.: 1 / Fragment: 25 residue peptide (residues 612-629)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P29352, protein-tyrosine-phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 293 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
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, Mumenthaler, Hermannstructure solution
DYANA1.5Guentert, Mumenthaler, Hermannrefinement
RefinementMethod: simulated annealing, torsional angle dynmaics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 25

+
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