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- PDB-1ayc: CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2... -

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Basic information

Entry
Database: PDB / ID: 1ayc
TitleCRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE
Components
  • PEPTIDE PDGFR-740
  • PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
KeywordsHYDROLASE(SH2 DOMAIN)
Function / homology
Function and homology information


metanephric glomerular mesangium development / response to ceramide / Signaling by PDGF / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Co-inhibition by BTLA / platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / PI-3K cascade:FGFR1 ...metanephric glomerular mesangium development / response to ceramide / Signaling by PDGF / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Co-inhibition by BTLA / platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / platelet-derived growth factor beta-receptor activity / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / cell migration involved in vasculogenesis / Tie2 Signaling / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / PECAM1 interactions / Interleukin-20 family signaling / smooth muscle cell chemotaxis / Signaling by CSF3 (G-CSF) / cardiac vascular smooth muscle cell differentiation / GAB1 signalosome / PI3K Cascade / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Co-inhibition by CTLA4 / Regulation of RUNX1 Expression and Activity / metanephric glomerular capillary formation / Interleukin-6 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / GPVI-mediated activation cascade / Spry regulation of FGF signaling / Co-inhibition by PD-1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Signaling by SCF-KIT / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / positive regulation of signal transduction / platelet-derived growth factor binding / negative regulation of hormone secretion / RAF/MAP kinase cascade / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / PIP3 activates AKT signaling / retina vasculature development in camera-type eye / genitalia development / Platelet sensitization by LDL / ruffle assembly / atrioventricular canal development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of cell adhesion mediated by integrin / Interleukin-3, Interleukin-5 and GM-CSF signaling / smooth muscle tissue development / RET signaling / cardiac myofibril assembly / tissue homeostasis / positive regulation of chemotaxis / negative regulation of neutrophil activation / cerebellar cortex formation / positive regulation of hormone secretion / regulation of protein export from nucleus / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / hormone metabolic process / negative regulation of chondrocyte differentiation / face morphogenesis / platelet formation / positive regulation of smooth muscle cell migration / skeletal system morphogenesis / positive regulation of DNA biosynthetic process / triglyceride metabolic process / adrenal gland development / megakaryocyte development / negative regulation of type I interferon production / organ growth / peptide hormone receptor binding / blood vessel development / positive regulation of calcium ion import / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / platelet-derived growth factor receptor signaling pathway / positive regulation of MAP kinase activity / inner ear development / Bergmann glial cell differentiation / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / regulation of MAPK cascade / phosphoprotein phosphatase activity / fibroblast growth factor receptor signaling pathway
Similarity search - Function
Platelet-derived growth factor receptor beta / Platelet-derived growth factor receptor Ig-like domain 4 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / SH2 domain / SHC Adaptor Protein / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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
Platelet-derived growth factor receptor beta / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLee, C.-H. / Kuriyan, J.
Citation
Journal: Structure / Year: 1994
Title: Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase.
Authors: Lee, C.H. / Kominos, D. / Jacques, S. / Margolis, B. / Schlessinger, J. / Shoelson, S.E. / Kuriyan, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1993
Title: Structures of Sh2 and SH3 Domains
Authors: Kuriyan, J. / Cowburn, D.
#3: Journal: 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.R. / 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
DepositionMay 15, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: 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: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
P: PEPTIDE PDGFR-740


Theoretical massNumber of molelcules
Total (without water)12,7572
Polymers12,7572
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-14 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.200, 62.200, 74.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)


Mass: 11528.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P35235, protein-tyrosine-phosphatase
#2: Protein/peptide PEPTIDE PDGFR-740


Mass: 1228.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P05622
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1protein1reservoir
320 %PEG40001reservoir
4100 mMMES1reservoir
2peptide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 6914 / % possible obs: 96 % / Num. measured all: 43918 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / % possible obs: 90.9 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 5362
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 4 63 900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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