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- PDB-1yi6: C-term tail segment of human tyrosine kinase (258-533) -

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Basic information

Entry
Database: PDB / ID: 1yi6
TitleC-term tail segment of human tyrosine kinase (258-533)
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / SRC / TYROSINE KINASE / PHOSPHORYLATION / REGULATION / SH2 / SH3
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 / intestinal epithelial cell development / regulation of vascular permeability / 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 / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / branching involved in mammary gland duct morphogenesis / response to acidic pH / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / positive regulation of podosome assembly / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / 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 / PECAM1 interactions / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / protein tyrosine kinase activator activity / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / GAB1 signalosome / positive regulation of protein serine/threonine kinase activity / negative regulation of hippo signaling
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: 2 Å
AuthorsFleury, D. / Sarubbi, E. / Courjaud, A. / Guitton, J.D. / Ducruix, A.
CitationJournal: To be published
Title: Structure of the unphosphorylated C-terminal tail segment of the SRC kinase and its role in SRC activity regulation
Authors: Fleury, D. / Sarubbi, E. / Courjaud, A. / Guitton, J.D. / Ducruix, A.
History
DepositionJan 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)63,6332
Polymers63,6332
Non-polymers00
Water9,638535
1
A: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)31,8161
Polymers31,8161
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)31,8161
Polymers31,8161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.985, 63.421, 76.693
Angle α, β, γ (deg.)90.00, 109.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / p60-Src / c-Src / PROTEIN TYROSINE KINASE


Mass: 31816.316 Da / Num. of mol.: 2 / Fragment: residues 258-533
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.: 535 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 21, 2000
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→19.97 Å / Num. all: 39386 / Num. obs: 37400 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.2 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.069 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3910 / Rsym value: 0.205 / % possible all: 93.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2src

2src


Resolution: 2→19 Å / σ(F): 1 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1959 5 %random
Rwork0.216 ---
all0.226 39359 --
obs0.216 37399 98 %-
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 0 535 4995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.46
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.04 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2-2.140.2973500.234660596
2.14-2.320.2643450.215663796
2.32-2.590.2513460.216667298
2.59-3.050.2413670.2236724100
3.05-4.260.2333430.26816100
4.26-190.2482080.231394590

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