[English] 日本語
Yorodumi
- PDB-1aot: NMR STRUCTURE OF THE FYN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aot
TitleNMR STRUCTURE OF THE FYN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROSYL PEPTIDE, MINIMIZED AVERAGE STRUCTURE
Components
  • FYN PROTEIN-TYROSINE KINASE
  • PHOSPHOTYROSYL PEPTIDE
KeywordsCOMPLEX (PROTO-ONCOGENE/EARLY PROTEIN) / SH2 DOMAIN / SIGNAL TRANSDUCTION / PEPTIDE COMPLEX / COMPLEX (PROTO-ONCOGENE-EARLY PROTEIN) / COMPLEX (PROTO-ONCOGENE-EARLY PROTEIN) complex
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / Co-stimulation by CD28 / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / activated T cell proliferation / FLT3 signaling through SRC family kinases / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / response to amyloid-beta / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / glial cell projection / FCGR activation / cellular response to glycine / host cell membrane / ephrin receptor signaling pathway / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / alpha-tubulin binding / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to platelet-derived growth factor stimulus / T cell costimulation / Signaling by ERBB2 / ephrin receptor binding / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / negative regulation of angiogenesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / learning / actin filament / Cell surface interactions at the vascular wall / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / negative regulation of inflammatory response to antigenic stimulus / non-specific protein-tyrosine kinase / G protein-coupled receptor binding / modulation of chemical synaptic transmission / neuron migration / protein catabolic process / Signaling by SCF-KIT / negative regulation of protein catabolic process / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / tau protein binding / positive regulation of neuron projection development / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / VEGFA-VEGFR2 Pathway / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to amyloid-beta / Signaling by CSF1 (M-CSF) in myeloid cells
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / : / Fyn/Yrk, SH3 domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / : / Fyn/Yrk, SH3 domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain / SHC Adaptor Protein / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Middle T antigen / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
Hamster polyomavirus
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING
AuthorsMulhern, T.D. / Shaw, G.L. / Morton, C.J. / Day, A.J. / Campbell, I.D.
Citation
Journal: Structure / Year: 1997
Title: The SH2 domain from the tyrosine kinase Fyn in complex with a phosphotyrosyl peptide reveals insights into domain stability and binding specificity.
Authors: Mulhern, T.D. / Shaw, G.L. / Morton, C.J. / Day, A.J. / Campbell, I.D.
#1: Journal: Eur.Biophys.J. / Year: 1996
Title: Solution Studies of the Sh2 Domain from the Fyn Tyrosine Kinase: Secondary Structure, Backbone Dynamics and Protein Association
Authors: Pintar, A. / Hensmann, M. / Jumel, K. / Pitkeathly, M. / Harding, S.E. / Campbell, I.D.
History
DepositionJul 10, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: FYN PROTEIN-TYROSINE KINASE
P: PHOSPHOTYROSYL PEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,7732
Polymers13,7732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200LEAST VIOLATIONS
Representative

-
Components

#1: Protein FYN PROTEIN-TYROSINE KINASE / SRC HOMOLOGY 2 DOMAIN


Mass: 12299.815 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN / Mutation: C97S, C98S, C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: LYSS / Plasmid: PRK172 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): LYSS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06241, EC: 2.7.1.112
#2: Protein/peptide PHOSPHOTYROSYL PEPTIDE


Mass: 1473.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hamster polyomavirus / Genus: Polyomavirus / References: UniProt: P03079
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141HSQC
151NOESY-HSQC
161TOCSY-HSQC
171CBCA(CO)NH
181(H)CCH-TOCSY
191XF-NOESY
1101XF-TOCSY

-
Sample preparation

Sample conditionspH: 6 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built OMEGAHome-builtOMEGA5001
Home-built OMEGAHome-builtOMEGA6002
Home-built OMEGAHome-builtOMEGA7503

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST VIOLATIONS / Conformers calculated total number: 200 / Conformers submitted total number: 1

+
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