[English] 日本語
Yorodumi
- PDB-2rsy: Solution structure of the SH2 domain of Csk in complex with a pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rsy
TitleSolution structure of the SH2 domain of Csk in complex with a phosphopeptide from Cbp
Components
  • Phosphoprotein associated with glycosphingolipid-enriched microdomains 1
  • Tyrosine-protein kinase CSK
KeywordsTRANSFERASE/SIGNALING PROTEIN / SH2 domain / Csk / Cbp / solution structure / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


GAB1 signalosome / Co-inhibition by PD-1 / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of T cell activation / adherens junction organization ...GAB1 signalosome / Co-inhibition by PD-1 / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of T cell activation / adherens junction organization / transmembrane receptor protein tyrosine kinase adaptor activity / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / regulation of T cell activation / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / negative regulation of T cell receptor signaling pathway / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / oligodendrocyte differentiation / SH2 domain binding / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / intracellular signal transduction / membrane raft / negative regulation of cell population proliferation / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 / Phosphoprotein associated with glycosphingolipid-enriched / CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 / Phosphoprotein associated with glycosphingolipid-enriched / CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase CSK / Phosphoprotein associated with glycosphingolipid-enriched microdomains 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailstarget function, model1
AuthorsTanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y. / Yokogawa, D. / Debenecker, M. / Nakagawa, A. ...Tanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y. / Yokogawa, D. / Debenecker, M. / Nakagawa, A. / Okada, M. / Ikegami, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains.
Authors: Tanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y.H. / Yokogawa, D. / Dobenecker, M.W. / Nakagawa, A. / Okada, M. / Ikegami, T.
History
DepositionSep 10, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase CSK
B: Phosphoprotein associated with glycosphingolipid-enriched microdomains 1


Theoretical massNumber of molelcules
Total (without water)15,7372
Polymers15,7372
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)20 / 100target function
RepresentativeModel #1target function

-
Components

#1: Protein Tyrosine-protein kinase CSK / C-Src kinase


Mass: 11473.135 Da / Num. of mol.: 1 / Fragment: Src homology 2 domain, UNP residues 80-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Csk / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3)
References: UniProt: P32577, non-specific protein-tyrosine kinase
#2: Protein/peptide Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 / Csk-binding protein / Transmembrane phosphoprotein Cbp


Mass: 4263.566 Da / Num. of mol.: 1 / Fragment: Cbp, UNP residues 288-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pag1, Cbp, Pag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JM80
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1313D HN(CA)CB
1433D HN(CA)CB
1513D CBCA(CO)NH
1633D CBCA(CO)NH
1713D HNCO
1833D HNCO
1913D HN(CA)CO
11033D HN(CA)CO
11113D HBHA(CO)NH
11233D HBHA(CO)NH
11323D 1H-15N TOCSY
11443D 1H-15N TOCSY
11552D 1H-13C HSQC
11662D 1H-13C HSQC
11752D 1H-13C HSQC aromatic
11862D 1H-13C HSQC aromatic
11953D 1H-13C NOESY aromatic
12063D 1H-13C NOESY aromatic
12152D DQF-COSY
12213D C(CO)NH
12333D C(CO)NH
12413D H(CCO)NH
12533D H(CCO)NH
12653D (H)CCH-TOCSY
12763D (H)CCH-TOCSY
12823D 1H-15N NOESY
12943D 1H-15N NOESY
13053D 1H-13C NOESY
13163D 1H-13C NOESY
13252D CBHD
13362D CBHD
13452D CBHE
13562D CBHE
13653D 13C-filtered/13C-edited NOESY
13763D 13C-filtered/13C-edited NOESY
13833D 13C,15N-filtered/15N-edited NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-13C; U-15N] Csk SH2 domain-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 0.5-1.0 mM Cbp phosphopeptide-4, 90 % H2O-5, 10 % [U-99% 2H] D2O-6, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM [U-15N] Csk SH2 domain-7, 20 mM sodium phosphate-8, 50 mM sodium chloride-9, 0.5-1.0 mM Cbp phosphopeptide-10, 90 % H2O-11, 10 % [U-99% 2H] D2O-12, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1.0 mM [U-13C; U-15N] Cbp phosphopeptide-13, 20 mM sodium phosphate-14, 50 mM sodium chloride-15, 0.5-1.0 mM Csk SH2 domain-16, 90 % H2O-17, 10 % [U-99% 2H] D2O-18, 90% H2O/10% D2O90% H2O/10% D2O
40.5-1.0 mM [U-15N] Cbp phosphopeptide-19, 20 mM sodium phosphate-20, 50 mM sodium chloride-21, 0.5-1.0 mM Csk SH2 domain-22, 90 % H2O-23, 10 % [U-99% 2H] D2O-24, 90% H2O/10% D2O90% H2O/10% D2O
50.5-1.0 mM [U-13C; U-15N] Csk SH2 domain-25, 20 mM sodium phosphate-26, 50 mM sodium chloride-27, 0.5-1.0 mM Cbp phosphopeptide-28, 90 % H2O-29, 10 % [U-99% 2H] D2O-30, 100% D2O100% D2O
60.5-1.0 mM [U-13C; U-15N] Cbp phosphopeptide-31, 20 mM sodium phosphate-32, 50 mM sodium chloride-33, 0.5-1.0 mM Csk SH2 domain-34, 90 % H2O-35, 10 % [U-2H] D2O-36, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCsk SH2 domain-1[U-13C; U-15N]0.5-1.01
20 mMsodium phosphate-21
50 mMsodium chloride-31
mMCbp phosphopeptide-40.5-1.01
90 %H2O-51
10 %D2O-6[U-99% 2H]1
mMCsk SH2 domain-7[U-15N]0.5-1.02
20 mMsodium phosphate-82
50 mMsodium chloride-92
mMCbp phosphopeptide-100.5-1.02
90 %H2O-112
10 %D2O-12[U-99% 2H]2
mMCbp phosphopeptide-13[U-13C; U-15N]0.5-1.03
20 mMsodium phosphate-143
50 mMsodium chloride-153
mMCsk SH2 domain-160.5-1.03
90 %H2O-173
10 %D2O-18[U-99% 2H]3
mMCbp phosphopeptide-19[U-15N]0.5-1.04
20 mMsodium phosphate-204
50 mMsodium chloride-214
mMCsk SH2 domain-220.5-1.04
90 %H2O-234
10 %D2O-24[U-99% 2H]4
mMCsk SH2 domain-25[U-13C; U-15N]0.5-1.05
20 mMsodium phosphate-265
50 mMsodium chloride-275
mMCbp phosphopeptide-280.5-1.05
90 %H2O-295
10 %D2O-30[U-99% 2H]5
mMCbp phosphopeptide-31[U-13C; U-15N]0.5-1.06
20 mMsodium phosphate-326
50 mMsodium chloride-336
mMCsk SH2 domain-340.5-1.06
90 %H2O-356
10 %D2O-36[U-2H]6
Sample conditionsIonic strength: 0.076 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichgeometry optimization
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2935 / NOE intraresidue total count: 604 / NOE long range total count: 1000 / NOE medium range total count: 552 / NOE sequential total count: 779
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0043 Å / Distance rms dev error: 0.0005 Å

+
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