[English] 日本語
Yorodumi
- PDB-2k7a: Ensemble Structures of the binary complex between the SH3 and SH2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k7a
TitleEnsemble Structures of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase.
Components
  • SH2 domain of Tyrosine-protein kinase ITK/TSK
  • SH3 domain of Tyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE / SH3 / SH2 / novel / cis / ATP-binding / Cell membrane / Kinase / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Zinc / Zinc-finger
Function / homology
Function and homology information


Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction ...Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / protein phosphorylation / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / SH2 domain / SHC Adaptor Protein / SH3 Domains / PH domain ...Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / SH2 domain / SHC Adaptor Protein / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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. / PH-like domain superfamily / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsAndreotti, A.H. / Severin, A.J. / Fulton, D.B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
Authors: Severin, A. / Joseph, R.E. / Boyken, S. / Fulton, D.B. / Andreotti, A.H.
History
DepositionAug 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 domain of Tyrosine-protein kinase ITK/TSK
B: SH2 domain of Tyrosine-protein kinase ITK/TSK


Theoretical massNumber of molelcules
Total (without water)20,0342
Polymers20,0342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area9600 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein SH3 domain of Tyrosine-protein kinase ITK/TSK / T-cell-specific kinase / IL-2-inducible T-cell kinase / Kinase EMT / Kinase TLK


Mass: 7355.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Production host: Escherichia coli (E. coli)
References: UniProt: Q03526, non-specific protein-tyrosine kinase
#2: Protein SH2 domain of Tyrosine-protein kinase ITK/TSK / T-cell-specific kinase / IL-2-inducible T-cell kinase / Kinase EMT / Kinase TLK


Mass: 12678.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Production host: Escherichia coli (E. coli)
References: UniProt: Q03526, non-specific protein-tyrosine kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11112D 1H-15N IPAP
11213D HNCA COSY
11312D 1H-15N IPAP
11413D HNCA COSY
1151(HB)CB(CGCDCE)HE
1161(HB)CB(CGCD)HD
11722D 1H-15N HSQC
11822D 1H-13C HSQC
11923D CBCA(CO)NH
12023D HNCO
12123D HN(CA)CB
12223D HN(CA)CB
12323D HBHA(CO)NH
12423D (H)CCH-TOCSY
12523D 1H-15N NOESY
12623D 1H-15N TOCSY
12723D 1H-13C NOESY
12822D 1H-15N IPAP
12922D 1H-15N IPAP
1302(HB)CB(CGCDCE)HE
1312(HB)CB(CGCD)HD
13222D 1H-15N HSQC
13332D 1H-15N HSQC
13442D 1H-15N HSQC
13532D 1H-13C HSQC
13642D 1H-13C HSQC
13733D CBCA(CO)NH
13843D CBCA(CO)NH
13933D HNCO
14043D HNCO
14133D HNHA
14243D HNHA
14333D HN(CA)CB
14443D HN(CA)CB
14533D 1H-15N NOESY
14643D 1H-15N NOESY
14733D 1H-15N TOCSY
14843D 1H-15N TOCSY
14933D 1H-13C NOESY
15043D 1H-13C NOESY
1513(HB)CB(CGCD)HD
1524(HB)CB(CGCD)HD
1533(HB)CB(CGCDCE)HE
1544(HB)CB(CGCDCE)HE
15532D 1H-15N IPAP
15642D 1H-15N IPAP
15743D HNCA COSY
15843D HNCA COSY
15932D 1H-15N IPAP
16042D 1H-15N IPAP
16133D HBHA(CO)NH
16243D HBHA(CO)NH
16333D (H)CCH-TOCSY
16443D (H)CCH-TOCSY
16532D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
13.4 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 1.5 mM Itk SH2 domain, 95% H2O/5% D2O95% H2O/5% D2O
23.4 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 1.5 mM Itk SH3 domain, 95% H2O/5% D2O95% H2O/5% D2O
31.5 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 3.4 mM Itk SH3 domain, 95% H2O/5% D2O95% H2O/5% D2O
41.5 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 3.4 mM Itk SH2 domain, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.4 mMItk SH3 domain[U-100% 13C; U-100% 15N]1
1.5 mMItk SH2 domain1
3.4 mMItk SH2 domain[U-100% 13C; U-100% 15N]2
1.5 mMItk SH3 domain2
1.5 mMItk SH2 domain[U-100% 13C; U-100% 15N]3
3.4 mMItk SH3 domain3
1.5 mMItk SH3 domain[U-100% 13C; U-100% 15N]4
3.4 mMItk SH2 domain4
Sample conditionsIonic strength: 75 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avii / Manufacturer: Bruker / Model: Avii / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
xplor-nih2.19Brunger A. T. et.al.refinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refine.py script from xplor-nih 2.19
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 20 / Representative conformer: 1

+
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