[English] 日本語
Yorodumi
- PDB-5hck: HUMAN HCK SH3 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hck
TitleHUMAN HCK SH3 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsHEMATOPOIETIC CELL KINASE
KeywordsTRANSFERASE / SH3 / PROTEIN TYROSINE KINASE / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


leukocyte degranulation / innate immune response-activating signaling pathway / respiratory burst after phagocytosis / leukocyte migration involved in immune response / regulation of podosome assembly / FLT3 signaling through SRC family kinases / regulation of phagocytosis / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / innate immune response-activating signaling pathway / respiratory burst after phagocytosis / leukocyte migration involved in immune response / regulation of podosome assembly / FLT3 signaling through SRC family kinases / regulation of phagocytosis / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / transport vesicle / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / lipopolysaccharide-mediated signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / integrin-mediated signaling pathway / cell projection / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / peptidyl-tyrosine phosphorylation / caveola / cytoplasmic side of plasma membrane / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein autophosphorylation / regulation of inflammatory response / protein tyrosine kinase activity / cell differentiation / cytoskeleton / lysosome / cell adhesion / intracellular signal transduction / protein phosphorylation / inflammatory response / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase HCK, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...Tyrosine-protein kinase HCK, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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 kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DG, SA
AuthorsHorita, D.A. / Baldisseri, D.M. / Zhang, W. / Altieri, A.S. / Smithgall, T.E. / Gmeiner, W.H. / Byrd, R.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Solution structure of the human Hck SH3 domain and identification of its ligand binding site.
Authors: Horita, D.A. / Baldisseri, D.M. / Zhang, W. / Altieri, A.S. / Smithgall, T.E. / Gmeiner, W.H. / Byrd, R.A.
History
DepositionMar 9, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 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: HEMATOPOIETIC CELL KINASE


Theoretical massNumber of molelcules
Total (without water)8,2401
Polymers8,2401
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)1 / 50MINIMIZED AVERAGE STRUCTURE
Representative

-
Components

#1: Protein HEMATOPOIETIC CELL KINASE / HCK


Mass: 8240.034 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: RESIDUES G72-E143 OF HUMAN HCK / Plasmid: PET-14B / Gene (production host): RESIDUES G72-E143 OF HUMAN HCK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS
References: UniProt: P08631, non-specific protein-tyrosine kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE JRNL ARTICLE

-
Sample preparation

Sample conditionspH: 6.25 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DG, SA / Software ordinal: 1
Details: PRESENTED ENSEMBLE WAS CALCULATED USING NOE/DIHEDRAL AND 1H AND 13C CHEMICAL SHIFT RESTRAINTS.
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE / Conformers calculated total number: 50 / Conformers submitted total number: 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