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

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Basic information

Entry
Database: PDB / ID: 1aya
TitleCRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE
Components
  • PEPTIDE PDGFR-1009
  • PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
KeywordsHYDROLASE(SH2 DOMAIN)
Function / homology
Function and homology information


metanephric glomerular mesangium development / platelet-derived growth factor-activated receptor activity / cell migration involved in coronary angiogenesis / metanephric mesenchymal cell migration / metanephric glomerular mesangial cell proliferation involved in metanephros development / response to ceramide / platelet-derived growth factor beta-receptor activity / metanephric comma-shaped body morphogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / metanephric glomerular capillary formation ...metanephric glomerular mesangium development / platelet-derived growth factor-activated receptor activity / cell migration involved in coronary angiogenesis / metanephric mesenchymal cell migration / metanephric glomerular mesangial cell proliferation involved in metanephros development / response to ceramide / platelet-derived growth factor beta-receptor activity / metanephric comma-shaped body morphogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / metanephric glomerular capillary formation / lung growth / smooth muscle cell chemotaxis / cardiac vascular smooth muscle cell differentiation / positive regulation of hepatic stellate cell activation / cell migration involved in vasculogenesis / aorta morphogenesis / negative regulation of hormone secretion / positive regulation of signal transduction / retina vasculature development in camera-type eye / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / platelet-derived growth factor binding / glycosaminoglycan biosynthetic process / phosphatidylinositol metabolic process / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / genitalia development / abortive mitotic cell cycle / cardiac myofibril assembly / negative regulation of growth hormone secretion / positive regulation of chemotaxis / atrioventricular canal development / vascular endothelial growth factor binding / positive regulation of ossification / ruffle assembly / negative regulation of cell adhesion mediated by integrin / smooth muscle tissue development / response to fluid shear stress / hormone metabolic process / cerebellar cortex formation / positive regulation of hormone secretion / non-membrane spanning protein tyrosine phosphatase activity / regulation of protein export from nucleus / organ growth / phospholipase binding / multicellular organismal reproductive process / platelet-derived growth factor receptor binding / D1 dopamine receptor binding / negative regulation of chondrocyte differentiation / triglyceride metabolic process / adrenal gland development / growth factor binding / megakaryocyte development / positive regulation of Rho protein signal transduction / peptide hormone receptor binding / intrinsic component of plasma membrane / face morphogenesis / skeletal system morphogenesis / ERBB signaling pathway / positive regulation of DNA biosynthetic process / tissue homeostasis / platelet formation / positive regulation of calcium ion import / positive regulation of smooth muscle cell migration / blood vessel development / platelet-derived growth factor receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase activity / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of interferon-beta production / inner ear development / nitrogen compound metabolic process / insulin receptor substrate binding / Bergmann glial cell differentiation / phosphoprotein phosphatase activity / positive regulation of phosphoprotein phosphatase activity / phosphatidylinositol 3-kinase binding / regulation of cell adhesion mediated by integrin / peptidyl-tyrosine dephosphorylation / negative regulation of insulin secretion / homeostasis of number of cells within a tissue / neurotrophin TRK receptor signaling pathway / regulation of protein-containing complex assembly / embryonic organ development / regulation of peptidyl-tyrosine phosphorylation / response to hyperoxia / positive regulation of collagen biosynthetic process / regulation of actin cytoskeleton organization / protein tyrosine kinase binding / positive regulation of phospholipase C activity / axonogenesis / positive regulation of tumor necrosis factor production / hormone-mediated signaling pathway / positive regulation of insulin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / response to retinoic acid / cell chemotaxis / positive regulation of interleukin-6 production / phosphatidylinositol-mediated signaling
Immunoglobulin / Platelet-derived growth factor receptor beta / Immunoglobulin subtype 2 / Immunoglobulin subtype / Tyrosine-protein kinase, receptor class III, conserved site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulin-like domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / Protein-tyrosine phosphatase, non-receptor type-6, -11 ...Immunoglobulin / Platelet-derived growth factor receptor beta / Immunoglobulin subtype 2 / Immunoglobulin subtype / Tyrosine-protein kinase, receptor class III, conserved site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulin-like domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / Immunoglobulin-like fold / Protein-tyrosine phosphatase, active site / Protein kinase, ATP binding site / Protein kinase domain / Tyrosine-protein kinase, catalytic domain / Protein-tyrosine phosphatase, catalytic / Protein-tyrosine phosphatase-like / SH2 domain / SH2 domain superfamily / Immunoglobulin-like domain superfamily / PTP type protein phosphatase / Tyrosine specific protein phosphatases domain / SH2 domain / SHC Adaptor Protein / 2-Layer Sandwich / Alpha Beta
Platelet-derived growth factor receptor beta / Tyrosine-protein phosphatase non-receptor type 11
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.05 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 15, 1994-
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
P: PEPTIDE PDGFR-1009
B: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
Q: PEPTIDE PDGFR-1009


Theoretical massNumber of molelcules
Total (without water)25,6594
Polymers25,6594
Non-polymers00
Water2,540141
1
A: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
P: PEPTIDE PDGFR-1009


Theoretical massNumber of molelcules
Total (without water)12,8292
Polymers12,8292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-13 kcal/mol
Surface area5950 Å2
MethodPISA
2
B: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
Q: PEPTIDE PDGFR-1009


Theoretical massNumber of molelcules
Total (without water)12,8292
Polymers12,8292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-13 kcal/mol
Surface area5590 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)33.800, 52.700, 56.400
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11528.979 Da / Num. of mol.: 2
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-1009


Mass: 1300.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P05622
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
315 %PEG40001reservoir
4100 mMMES1reservoir
1protein1reservoir
2peptide1reservoir
5protein1reservoir
61
71

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 30 Å / Num. all: 26661 / Num. obs: 11145 / % possible obs: 90.2 % / Rmerge(I) obs: 0.084

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.05→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.18 -
Obs0.18 10547
Refinement stepCycle: LAST / Resolution: 2.05→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 141 1872
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3
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: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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