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- PDB-3d7t: Structural basis for the recognition of c-Src by its inactivator Csk -

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Basic information

Entry
Database: PDB / ID: 3d7t
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 SRC TYROSINE KINASE / ATP-binding / Cytoplasm / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / SH2 domain / SH3 domain / Tyrosine-protein kinase / Alternative splicing / 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 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome ...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 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of phagocytosis / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / osteoclast development / cellular response to peptide hormone stimulus / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / progesterone receptor signaling pathway / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / RHOH GTPase cycle / PD-1 signaling / GAB1 signalosome / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / Negative regulation of FLT3 / protein tyrosine kinase binding / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / Integrin signaling / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / Signaling by high-kinase activity BRAF mutants / non-membrane spanning protein tyrosine kinase activity / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / 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 / cell junction / T cell receptor signaling pathway / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / adaptive immune response / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / negative regulation of cell population proliferation / phosphorylation / signaling receptor binding / protein phosphorylation / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / ATP binding / membrane
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 / Proto-oncogene tyrosine-protein kinase Src / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.899 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 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase CSK
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6364
Polymers62,7032
Non-polymers9332
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosine-protein kinase CSK
hetero molecules

B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6364
Polymers62,7032
Non-polymers9332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area3110 Å2
ΔGint-9 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.646, 99.646, 137.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 29976.562 Da / Num. of mol.: 1 / Fragment: Csk kinase domain / Mutation: K361A/K362A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P41240, non-specific protein-tyrosine kinase
#2: Protein Proto-oncogene tyrosine-protein kinase Src / / pp60c-src / p60-Src / c-Src


Mass: 32726.645 Da / Num. of mol.: 1 / 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) / Strain (production host): BL21 DE3
References: UniProt: P00523, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 17942 / % possible obs: 99.5 %

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.899→45.686 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 0.2 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 857 5.1 %
Rwork0.237 --
obs0.239 16816 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.755 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 204.91 Å2 / Biso mean: 107.873 Å2 / Biso min: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-13.908 Å2-0 Å2-0 Å2
2--13.908 Å2-0 Å2
3----27.815 Å2
Refinement stepCycle: LAST / Resolution: 2.899→45.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 70 0 4174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074283
X-RAY DIFFRACTIONf_angle_d1.1485816
X-RAY DIFFRACTIONf_chiral_restr0.081627
X-RAY DIFFRACTIONf_plane_restr0.005728
X-RAY DIFFRACTIONf_dihedral_angle_d18.7451573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.899-3.0810.361360.3052314245083
3.081-3.3190.3131310.2782551268290
3.319-3.6520.3121440.2572652279695
3.652-4.1810.2521560.222733288996
4.181-5.2660.2861390.2112798293798
5.266-45.6920.2591510.2362911306298

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