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- PDB-8vcf: Crystal structure of Superbinder Src SH2 domain with Cysteine to ... -

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Basic information

Entry
Database: PDB / ID: 8vcf
TitleCrystal structure of Superbinder Src SH2 domain with Cysteine to Serine mutations
ComponentsIsoform 3 of Proto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / SH2 DOMAIN / SUPERBINDER 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 / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / 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 / connexin binding / Activated NTRK3 signals through PI3K / osteoclast development / 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 / EPH-Ephrin signaling / positive regulation of podosome assembly / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / Signal regulatory protein family interactions / podosome / odontogenesis / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / leukocyte migration / Signaling by ALK / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / 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 / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of cell-cell adhesion / Recycling pathway of L1 / PECAM1 interactions / uterus development / regulation of heart rate by cardiac conduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / negative regulation of anoikis / Long-term potentiation / signaling receptor activator activity / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / positive regulation of protein serine/threonine kinase activity / GAB1 signalosome / 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 / forebrain development / Downregulation of ERBB4 signaling / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / InlA-mediated entry of Listeria monocytogenes into host cells / phospholipase binding / 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 / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / ionotropic glutamate receptor binding
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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHashem, A. / Nyovanie, S. / Patskovsky, Y. / Oltean, N. / 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


Theoretical massNumber of molelcules
Total (without water)14,4071
Polymers14,4071
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6160 Å2
Unit cell
Length a, b, c (Å)67.481, 67.481, 46.886
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: 14407.089 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 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.36 % / Description: PYRAMID
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOR DIFFUSION,SITTING DROP, TEMPERATURE 290K 0.2 M Ammonium Fluoride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 3, 2023 / Details: SI 111 CRYSTAL
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→46.89 Å / Num. obs: 19583 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.074 / Χ2: 0 / Net I/σ(I): 22.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 943 / Χ2: 0 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0257refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F59

4f59


Resolution: 1.5→33.74 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.965 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17664 601 3.1 %RANDOM
Rwork0.13733 ---
obs0.13853 18935 99.88 %-
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: 33.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 0 120 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013876
X-RAY DIFFRACTIONr_bond_other_d0.0010.017783
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.6431187
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5721808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.67221.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74315144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.314157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
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_it7.883.206433
X-RAY DIFFRACTIONr_mcbond_other7.8563.194432
X-RAY DIFFRACTIONr_mcangle_it7.3174.773540
X-RAY DIFFRACTIONr_mcangle_other7.3114.788541
X-RAY DIFFRACTIONr_scbond_it9.1873.742443
X-RAY DIFFRACTIONr_scbond_other9.1823.743443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8075.41647
X-RAY DIFFRACTIONr_long_range_B_refined7.76638.373988
X-RAY DIFFRACTIONr_long_range_B_other7.58737.575960
X-RAY DIFFRACTIONr_rigid_bond_restr20.89631659
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 39 -
Rwork0.209 1376 -
obs--100 %

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