[English] 日本語
Yorodumi
- PDB-1ayd: CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ayd
TitleCRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE
ComponentsPROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
KeywordsHYDROLASE(SH2 DOMAIN)
Function / homology
Function and homology information


PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Co-inhibition by BTLA / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / FRS-mediated FGFR1 signaling ...PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Co-inhibition by BTLA / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / PECAM1 interactions / Interleukin-20 family signaling / Signaling by CSF3 (G-CSF) / GAB1 signalosome / PI3K Cascade / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Co-inhibition by CTLA4 / Regulation of RUNX1 Expression and Activity / Interleukin-6 signaling / Downstream signal transduction / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / GPVI-mediated activation cascade / Spry regulation of FGF signaling / Co-inhibition by PD-1 / Signaling by SCF-KIT / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of signal transduction / negative regulation of hormone secretion / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / PIP3 activates AKT signaling / genitalia development / Platelet sensitization by LDL / 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 / RET signaling / 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 / triglyceride metabolic process / megakaryocyte development / negative regulation of type I interferon production / organ growth / peptide hormone receptor binding / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / platelet-derived growth factor receptor signaling pathway / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / regulation of MAPK cascade / phosphoprotein phosphatase activity / fibroblast growth factor receptor signaling pathway / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / cell adhesion molecule binding / negative regulation of T cell proliferation / hormone-mediated signaling pathway / phosphotyrosine residue binding / protein-tyrosine-phosphatase / homeostasis of number of cells within a tissue / positive regulation of mitotic cell cycle / axonogenesis / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / cellular response to epidermal growth factor stimulus / DNA damage checkpoint signaling / integrin-mediated signaling pathway / positive regulation of D-glucose import / insulin receptor binding / cellular response to mechanical stimulus / negative regulation of insulin secretion / receptor tyrosine kinase binding / lipid metabolic process / vasodilation / multicellular organism growth / epidermal growth factor receptor signaling pathway / positive regulation of tumor necrosis factor production / glucose homeostasis / signaling receptor complex adaptor activity / positive regulation of ERK1 and ERK2 cascade
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)


Theoretical massNumber of molelcules
Total (without water)11,5291
Polymers11,5291
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.200, 63.200, 76.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %satammonium sulfate1reservoir
2100 mMMES1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 8075 / % possible obs: 97 % / Num. measured all: 63420 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.24 Å / % possible obs: 92.1 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 6359
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 0 87 871
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_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: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more