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- PDB-3d7u: Structural basis for the recognition of c-Src by its inactivator Csk -

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Basic information

Entry
Database: PDB / ID: 3d7u
TitleStructural basis for the recognition of c-Src by its inactivator Csk
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • Tyrosine-protein kinase CSK
KeywordsTRANSFERASE / Csk c-Src Tyrosine kinase / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Lipoprotein / Myristate / Proto-oncogene
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 / Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity ...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 / Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / adherens junction organization / proline-rich region binding / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / Phosphorylation of CD3 and TCR zeta chains / protein kinase A catalytic subunit binding / negative regulation of intrinsic apoptotic signaling pathway / oligodendrocyte differentiation / negative regulation of interleukin-6 production / RHOH GTPase cycle / immune system process / Co-inhibition by PD-1 / GAB1 signalosome / progesterone receptor signaling pathway / T cell costimulation / Integrin signaling / Negative regulation of FLT3 / protein tyrosine kinase binding / negative regulation of extrinsic apoptotic signaling pathway / 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 / epidermal growth factor receptor signaling pathway / 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 / Signaling by BRAF and RAF1 fusions / cell junction / cell-cell junction / T cell receptor signaling pathway / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / protein phosphorylation / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
CSK-like, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily ...CSK-like, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / 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
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.111 Å
AuthorsLevinson, N.M. / Seeliger, M.A. / Cole, P.A. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural basis for the recognition of c-Src by its inactivator Csk.
Authors: Levinson, N.M. / Seeliger, M.A. / Cole, P.A. / Kuriyan, J.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase CSK
B: Proto-oncogene tyrosine-protein kinase Src
C: Tyrosine-protein kinase CSK
D: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)122,8524
Polymers122,8524
Non-polymers00
Water00
1
A: Tyrosine-protein kinase CSK
B: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)61,4262
Polymers61,4262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tyrosine-protein kinase CSK
D: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)61,4262
Polymers61,4262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.839, 135.839, 129.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Tyrosine-protein kinase CSK / C-SRC kinase / Protein-tyrosine kinase CYL


Mass: 29624.256 Da / Num. of mol.: 2 / Fragment: Csk kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSK / Production host: Escherichia coli (E. coli)
References: UniProt: P41240, non-specific protein-tyrosine kinase
#2: Protein Proto-oncogene tyrosine-protein kinase Src / pp60c-src / p60-Src / c-Src


Mass: 31801.605 Da / Num. of mol.: 2 / Fragment: c-Src kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli)
References: UniProt: P00523, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.62 Å3/Da / Density % sol: 78.1 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4.0117→46.8705 Å / Num. obs: 22041

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.111→46.866 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.67 / σ(F): 1.96 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.302 1053 5.14 %
Rwork0.294 19446 -
obs0.294 20499 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 123.071 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 271.05 Å2 / Biso mean: 191.051 Å2 / Biso min: 119.61 Å2
Baniso -1Baniso -2Baniso -3
1-16.564 Å2-0 Å2-0 Å2
2--16.564 Å2-0 Å2
3----33.129 Å2
Refinement stepCycle: LAST / Resolution: 4.111→46.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 0 0 8153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.028341
X-RAY DIFFRACTIONf_angle_d1.59211281
X-RAY DIFFRACTIONf_dihedral_angle_d21.6953102
X-RAY DIFFRACTIONf_chiral_restr0.0881232
X-RAY DIFFRACTIONf_plane_restr0.0081440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.111-4.2980.3661510.3632431258298
4.298-4.5240.2981280.3432436256499
4.524-4.8070.2861170.31924872604100
4.807-5.1780.3441330.3092409254299
5.178-5.6990.3511420.332463260599
5.699-6.5210.3141410.3072416255799
6.521-8.2090.2721280.2732408253698
8.209-46.8690.2471130.2362396250996

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