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- PDB-1yoj: Crystal structure of Src kinase domain -

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Basic information

Entry
Database: PDB / ID: 1yoj
TitleCrystal structure of Src kinase domain
Componentsproto-oncogene tyrosine-protein kinase SRC
KeywordsTRANSFERASE / protein tyrosine kinase
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / positive regulation of protein transport / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / positive regulation of integrin activation / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / regulation of vascular permeability / intestinal epithelial cell development / negative regulation of neutrophil activation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / focal adhesion assembly / cellular response to fluid shear stress / Co-stimulation by CD28 / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / response to acidic pH / branching involved in mammary gland duct morphogenesis / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / positive regulation of podosome assembly / DCC mediated attractive signaling / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / cellular response to peptide hormone stimulus / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to fatty acid / Regulation of KIT signaling / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / oogenesis / GP1b-IX-V activation signalling / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / Signaling by EGFR / stress fiber assembly / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / PECAM1 interactions / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / RHOU GTPase cycle / protein tyrosine kinase activator activity / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / Long-term potentiation / RET signaling / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / positive regulation of bone resorption
Similarity search - Function
: / 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 / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBreitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of active SRC kinase domain complexes
Authors: Breitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: proto-oncogene tyrosine-protein kinase SRC
B: proto-oncogene tyrosine-protein kinase SRC


Theoretical massNumber of molelcules
Total (without water)64,9002
Polymers64,9002
Non-polymers00
Water4,071226
1
A: proto-oncogene tyrosine-protein kinase SRC


Theoretical massNumber of molelcules
Total (without water)32,4501
Polymers32,4501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: proto-oncogene tyrosine-protein kinase SRC


Theoretical massNumber of molelcules
Total (without water)32,4501
Polymers32,4501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.867, 62.542, 73.902
Angle α, β, γ (deg.)100.52, 88.88, 89.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein proto-oncogene tyrosine-protein kinase SRC / p60-SRC / C-SRC


Mass: 32450.248 Da / Num. of mol.: 2 / Fragment: Src kinase domain / Mutation: S344N, A369S, Y418W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00075 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00075 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 51365 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.135 / Net I/σ(I): 6.8
Reflection shellResolution: 1.95→2.2 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.334 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: active Src kinase domain in complex with CGP77675

Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.395 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25811 2542 5 %RANDOM
Rwork0.21403 ---
obs0.2162 48107 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.07 Å2-0.11 Å2
2---1.7 Å20.11 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 0 226 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223701
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9825010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38423.787169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90715657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8661527
X-RAY DIFFRACTIONr_chiral_restr0.0990.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022774
X-RAY DIFFRACTIONr_nbd_refined0.2090.21657
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.29
X-RAY DIFFRACTIONr_mcbond_it1.0541.52319
X-RAY DIFFRACTIONr_mcangle_it1.67223623
X-RAY DIFFRACTIONr_scbond_it2.53331617
X-RAY DIFFRACTIONr_scangle_it3.8784.51387
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 191 -
Rwork0.242 3318 -
obs--88.43 %

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