[English] 日本語
Yorodumi
- PDB-1csk: THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1csk
TitleTHE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP
ComponentsC-SRC SH3 DOMAIN
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / negative regulation of phagocytosis / negative regulation of bone resorption / adherens junction organization / cellular response to peptide hormone stimulus / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation ...negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / negative regulation of phagocytosis / negative regulation of bone resorption / adherens junction organization / cellular response to peptide hormone stimulus / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / RHOH GTPase cycle / PD-1 signaling / GAB1 signalosome / Negative regulation of FLT3 / T cell costimulation / Integrin signaling / protein tyrosine kinase binding / non-specific protein-tyrosine kinase / Signaling by high-kinase activity BRAF mutants / non-membrane spanning protein tyrosine kinase activity / MAP2K and MAPK activation / negative regulation of ERK1 and ERK2 cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / T cell receptor signaling pathway / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / negative regulation of cell population proliferation / protein phosphorylation / extracellular exosome / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CSK-like, SH2 domain / SH3 Domains / 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 ...CSK-like, SH2 domain / SH3 Domains / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMathieu, M. / Wierenga, R.K.
CitationJournal: FEBS Lett. / Year: 1994
Title: The crystal structure of human CskSH3: structural diversity near the RT-Src and n-Src loop.
Authors: Borchert, T.V. / Mathieu, M. / Zeelen, J.P. / Courtneidge, S.A. / Wierenga, R.K.
History
DepositionMar 22, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-SRC SH3 DOMAIN
B: C-SRC SH3 DOMAIN
C: C-SRC SH3 DOMAIN
D: C-SRC SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)31,4084
Polymers31,4084
Non-polymers00
Water1448
1
A: C-SRC SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)7,8521
Polymers7,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-SRC SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)7,8521
Polymers7,8521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-SRC SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)7,8521
Polymers7,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-SRC SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)7,8521
Polymers7,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.900, 74.690, 125.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE FOUR MOLECULES ARE PACKED IN THE CELL AS A DIMER OF DIMERS, ONE DIMER BEING FORMED OF MOLECULES D AND A, AND THE OTHER OF MOLECULES B AND C.

-
Components

#1: Protein
C-SRC SH3 DOMAIN


Mass: 7851.946 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P41240, EC: 2.7.1.112
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTEA/HCl12
220 mM12NaCl
31 mMDTT12
41 mMEDTA12
51 mM12NaN3
610 mg/mlprotein11

-
Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. obs: 10807 / % possible obs: 94.8 % / Num. measured all: 60252 / Rmerge(I) obs: 0.083

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.278 -
Rwork0.224 -
obs0.224 9913
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 0 8 1832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 9913 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.9

+
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