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- PDB-1csk: THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR ... -

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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 T cell activation / adherens junction organization / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / negative regulation of T cell receptor signaling pathway ...negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of T cell activation / adherens junction organization / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / negative regulation of T cell receptor signaling pathway / Phosphorylation of CD3 and TCR zeta chains / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / oligodendrocyte differentiation / RHOH GTPase cycle / Co-inhibition by PD-1 / GAB1 signalosome / T cell costimulation / Integrin signaling / Negative regulation of FLT3 / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Signaling by high-kinase activity BRAF mutants / 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 tyrosine kinase activity / protein phosphatase binding / adaptive immune response / protein phosphorylation / intracellular signal transduction / negative regulation of cell population proliferation / extracellular exosome / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm / cytosol
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 ...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 / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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