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- PDB-8vcg: Mutant Src SH2 domain in complex with phosphotyrosine -

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Basic information

Entry
Database: PDB / ID: 8vcg
TitleMutant Src SH2 domain in complex with phosphotyrosine
ComponentsIsoform 3 of Proto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / SH2 DOMAIN / CELL SIGNALLING / PHOSPHOTYROSINE BINDING
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 / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity ...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 / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of integrin activation / Activated NTRK2 signals through FYN / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / 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 / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / podosome / odontogenesis / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / regulation of cell-cell adhesion / uterus development / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / protein tyrosine kinase activator activity / negative regulation of anoikis / signaling receptor activator activity / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / GAB1 signalosome / positive regulation of protein serine/threonine kinase activity / negative regulation of hippo signaling / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / negative regulation of protein-containing complex assembly / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / phospholipase binding / forebrain development / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / ephrin receptor binding / Signaling by ERBB2 / EPHB-mediated forward signaling / Integrin signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Downregulation of ERBB4 signaling
Similarity search - Function
: / 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 / 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 / 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
O-PHOSPHOTYROSINE / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsHashem, A. / Nyovanie, S. / Oltean, N. / Patskovska, L. / Patskovsky, Y. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243486-01A1 United States
CitationJournal: To Be Published
Title: Engineered Mutant Src Sh2 Domain
Authors: Hashem, A. / Nyovanie, S. / Patskovsky, Y. / Krogsgaard, M.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5812
Polymers14,3201
Non-polymers2611
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6460 Å2
Unit cell
Length a, b, c (Å)67.674, 67.674, 46.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Isoform 3 of Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 14320.010 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H12NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.3 % / Description: PYRAMID
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 0.2 M Ammonium Fluoride, 20% PEG 3350
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2023 / Details: SI 111 CRYSTAL
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.61→29.3 Å / Num. obs: 15693 / % possible obs: 99.4 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.5
Reflection shellResolution: 1.61→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1097 / Χ2: 0.56 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→29.3 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.494 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17569 472 3 %RANDOM
Rwork0.12215 ---
obs0.12392 15213 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.61→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 136 1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013912
X-RAY DIFFRACTIONr_bond_other_d0.0020.017825
X-RAY DIFFRACTIONr_angle_refined_deg1.81.6531238
X-RAY DIFFRACTIONr_angle_other_deg1.5221.5761909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.6620.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13915154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.288158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021031
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02213
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6123.096440
X-RAY DIFFRACTIONr_mcbond_other7.6113.092440
X-RAY DIFFRACTIONr_mcangle_it6.8274.595548
X-RAY DIFFRACTIONr_mcangle_other6.8214.6549
X-RAY DIFFRACTIONr_scbond_it12.0043.946472
X-RAY DIFFRACTIONr_scbond_other12.0453.956468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.0855.514688
X-RAY DIFFRACTIONr_long_range_B_refined9.90338.881065
X-RAY DIFFRACTIONr_long_range_B_other9.88937.5691026
X-RAY DIFFRACTIONr_rigid_bond_restr17.70231737
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.614→1.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 35 -
Rwork0.186 1057 -
obs--94.71 %

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