[English] 日本語
Yorodumi
- PDB-1byg: KINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1byg
TitleKINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WITH INHIBITOR STAUROSPORINE
ComponentsPROTEIN (C-TERMINAL SRC KINASE)
KeywordsTRANSFERASE / PROTEIN KINASE / C-TERMINAL SRC KINASE / PHOSPHORYLATION / STAUROSPORINE
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 / negative regulation of phagocytosis / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / 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 / negative regulation of phagocytosis / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / 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 / protein tyrosine kinase binding / T cell costimulation / Integrin signaling / 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / 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 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. ...CSK-like, SH2 domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAntson, A.A. / Lamers, M.B.A.C. / Scott, R.K. / Williams, D.H. / Hubbard, R.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporine.
Authors: Lamers, M.B. / Antson, A.A. / Hubbard, R.E. / Scott, R.K. / Williams, D.H.
History
DepositionOct 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (C-TERMINAL SRC KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6482
Polymers31,1821
Non-polymers4671
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.490, 120.580, 48.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PROTEIN (C-TERMINAL SRC KINASE) / CSK


Mass: 31181.918 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE C-TERMINAL HISTIDINE TAG WAS NOT OBSERVED IN THE DENSITY AND IS NOT PRESENT IN THE SEQRES.
Source: (gene. exp.) Homo sapiens (human)
Description: THE CDNA FOR THE CATALYTIC DOMAIN OF CSK WAS ISOLATED BY POLYMERASE CHAIN REACTION FROM GRANULOCYTE CDNA OBTAINED FROM HUMAN LUNG TISSUE. A HEXAHISTIDINE TAG WAS ENGINEERED AT THE C- ...Description: THE CDNA FOR THE CATALYTIC DOMAIN OF CSK WAS ISOLATED BY POLYMERASE CHAIN REACTION FROM GRANULOCYTE CDNA OBTAINED FROM HUMAN LUNG TISSUE. A HEXAHISTIDINE TAG WAS ENGINEERED AT THE C-TERMINUS TO AID PURIFICATION.
Cell: GRANULOCYTE / Organ: LUNG / Plasmid: PQE60-CSK / Gene (production host): CSK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P41240, EC: 2.7.1.112
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growpH: 9
Details: VAPOUR DIFFUSION, PROTEIN SOLUTION (10 MG/ML) CONTAINING 1MM STAUROSPORINE WAS MIXED IN 1:1 RATIO WITH THE RESERVOIR SOLUTION. THE RESERVOIR SOLUTION CONTAINED 0.2M MGCL2, 0.1M TRISHCL PH 9.0, 24% PEG 4000.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21 mMstaurosporine1drop
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH9.0
524 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRROR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 30746 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / % possible all: 61.8
Reflection shell
*PLUS
% possible obs: 61.8 %

-
Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMK

1fmk


Resolution: 2.4→20 Å / SU B: 10.8 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1007 10 %RANDOM
Rwork0.199 ---
obs-10089 93.6 %-
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 35 152 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.2
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.341.5
X-RAY DIFFRACTIONp_mcangle_it2.292
X-RAY DIFFRACTIONp_scbond_it4.584
X-RAY DIFFRACTIONp_scangle_it5.976
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.2610.3
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.63
X-RAY DIFFRACTIONp_staggered_tor18.620
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.730
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.2
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.3
X-RAY DIFFRACTIONp_mcbond_it1.51.34
X-RAY DIFFRACTIONp_scbond_it44.58
X-RAY DIFFRACTIONp_mcangle_it22.29
X-RAY DIFFRACTIONp_scangle_it65.97

+
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