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- PDB-1sha: CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 O... -

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Entry
Database: PDB / ID: 1sha
TitleCRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES
Components
  • PHOSPHOPEPTIDE A
  • V-SRC SH2 DOMAIN
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in vasculogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / aorta morphogenesis ...platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in vasculogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / smooth muscle adaptation / platelet-derived growth factor binding / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / cardiac myofibril assembly / Signaling by PDGF / positive regulation of chemotaxis / phospholipase C activator activity / platelet-derived growth factor receptor binding / positive regulation of smooth muscle cell migration / positive regulation of DNA biosynthetic process / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of calcium ion import / platelet-derived growth factor receptor signaling pathway / positive regulation of MAP kinase activity / positive regulation of smooth muscle cell proliferation / positive regulation of mitotic nuclear division / Downstream signal transduction / positive regulation of calcium-mediated signaling / lysosomal lumen / GTPase activator activity / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / cell chemotaxis / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / receptor protein-tyrosine kinase / positive regulation of reactive oxygen species metabolic process / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / protein tyrosine kinase activity / angiogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / positive regulation of cell migration / apical plasma membrane / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / protein kinase binding / enzyme binding / Golgi apparatus / signal transduction / ATP binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Platelet-derived growth factor receptor beta / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / SH2 domain / SHC Adaptor Protein / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : ...Platelet-derived growth factor receptor beta / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / SH2 domain / SHC Adaptor Protein / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / SH3 domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase transforming protein Src / Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsWaksman, G. / Kuriyan, J.
CitationJournal: Nature / Year: 1992
Title: Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides.
Authors: Waksman, G. / Kominos, D. / Robertson, S.C. / Pant, N. / Baltimore, D. / Birge, R.B. / Cowburn, D. / Hanafusa, H. / Mayer, B.J. / Overduin, M. / Resh, M.D. / Rios, C.B. / Silverman, L. / Kuriyan, J.
History
DepositionAug 18, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 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: V-SRC SH2 DOMAIN
B: PHOSPHOPEPTIDE A


Theoretical massNumber of molelcules
Total (without water)12,6722
Polymers12,6722
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area6280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.300, 57.500, 39.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein V-SRC SH2 DOMAIN


Mass: 11970.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P00524, EC: 2.7.1.112
#2: Protein/peptide PHOSPHOPEPTIDE A


Mass: 701.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P09619*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMprotein1drop
210 %PEG40001reservoir
3100 mMHEPES1reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.5→6 Å / Rfactor Rwork: 0.208 / Rfactor obs: 0.208 / σ(F): 2
Details: THE LOOP FROM RESIDUE 49 TO 53 IS DISORDERED AND IS NOT CLEARLY VISIBLE IN THE ELECTRON DENSITY.
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 4 58 939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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