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- PDB-1aot: NMR STRUCTURE OF THE FYN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROS... -

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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


response to singlet oxygen / negative regulation of hydrogen peroxide biosynthetic process / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / growth factor receptor binding / heart process / reelin-mediated signaling pathway / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / negative regulation of hydrogen peroxide biosynthetic process / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / growth factor receptor binding / heart process / reelin-mediated signaling pathway / regulation of glutamate receptor signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / CD28 co-stimulation / cellular response to L-glutamate / Platelet Adhesion to exposed collagen / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / positive regulation of protein localization to membrane / activated T cell proliferation / FLT3 signaling through SRC family kinases / positive regulation of cysteine-type endopeptidase activity / type 5 metabotropic glutamate receptor binding / negative regulation of dendritic spine maintenance / feeding behavior / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendrite morphogenesis / dendritic spine maintenance / Regulation of KIT signaling / leukocyte migration / CTLA4 inhibitory signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / tau-protein kinase activity / phospholipase activator activity / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / PECAM1 interactions / response to amyloid-beta / phospholipase binding / CD28 dependent PI3K/Akt signaling / Sema3A PAK dependent Axon repulsion / glial cell projection / cellular response to glycine / FCGR activation / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / host cell membrane / ephrin receptor signaling pathway / alpha-tubulin binding / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / forebrain development / Signaling by ERBB2 / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / negative regulation of protein ubiquitination / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / axon guidance / actin filament / Cell surface interactions at the vascular wall / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / protein catabolic process / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to amyloid-beta / disordered domain specific binding
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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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

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Sample preparation

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

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NMR measurement

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

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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

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