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- PDB-5zau: Complex of the human FYN SH3 and monobody binder -

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Basic information

Entry
Database: PDB / ID: 5zau
TitleComplex of the human FYN SH3 and monobody binder
Components
  • Monobody Binder
  • Tyrosine-protein kinase Fyn
KeywordsSIGNALING 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 / 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 ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / 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 / Platelet Adhesion to exposed collagen / cellular response to L-glutamate / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / G protein-coupled glutamate receptor signaling pathway / heart process / CD4 receptor binding / feeding behavior / positive regulation of protein localization to membrane / Nef and signal transduction / natural killer cell activation / Co-stimulation by CD28 / EPH-Ephrin signaling / DCC mediated attractive signaling / Nephrin family interactions / type 5 metabotropic glutamate receptor binding / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / negative regulation of dendritic spine maintenance / leukocyte migration / Regulation of KIT signaling / cellular response to peptide hormone stimulus / growth factor receptor binding / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / negative regulation of T cell activation / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / peptide hormone receptor binding / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / CD8 receptor binding / response to amyloid-beta / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / CD28 dependent PI3K/Akt signaling / vascular endothelial growth factor receptor signaling pathway / cellular response to glycine / ephrin receptor signaling pathway / positive regulation of protein targeting to membrane / negative regulation of T cell receptor signaling pathway / glial cell projection / T cell costimulation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / alpha-tubulin binding / ephrin receptor binding / postsynaptic density, intracellular component / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / T cell receptor binding / phospholipase binding / Signaling by ERBB2 / negative regulation of angiogenesis / EPHB-mediated forward signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / learning / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / response to cocaine / actin filament / negative regulation of inflammatory response to antigenic stimulus / non-membrane spanning protein tyrosine kinase activity / Regulation of signaling by CBL / Signaling by SCF-KIT / cellular response to growth factor stimulus / VEGFA-VEGFR2 Pathway / G protein-coupled receptor binding / Degradation of CDH1 / modulation of chemical synaptic transmission / cellular response to hydrogen peroxide / tau protein binding / Schaffer collateral - CA1 synapse / T cell receptor signaling pathway / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
Sulfolobus solfataricus (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsReddy, P.P. / Gulyani, A. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
TIFR India
CitationJournal: Elife / Year: 2020
Title: A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells.
Authors: Mukherjee, A. / Singh, R. / Udayan, S. / Biswas, S. / Reddy, P.P. / Manmadhan, S. / George, G. / Kumar, S. / Das, R. / Rao, B.M. / Gulyani, A.
History
DepositionFeb 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Monobody Binder


Theoretical massNumber of molelcules
Total (without water)13,8952
Polymers13,8952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area7200 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 6524.066 Da / Num. of mol.: 1 / Fragment: UNP residues 85-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli (E. coli)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Antibody Monobody Binder


Mass: 7370.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
153isotropic13D NOESY HSQC
164isotropic12D 1H-15N HSQC
175isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] FYN SH3 domain, 90% H2O/10% D2O15,13C_FYN90% H2O/10% D2O
solution21 mM [U-99% 13C; U-99% 15N] Monobody Binder, 90% H2O/10% D2O15,13C_F2990% H2O/10% D2O
solution31 mM [U-99% 15N; U-98% 2H] FYN SH3 domain, 1.5 mM Unlabeled Monobody Binder, 90% H2O/10% D2OComplex90% H2O/10% D2O
solution40.2 mM [U-99% 15N] FYN SH3 domain, 1 mM Unlabeled Monobody Binder, 90% H2O/10% D2O15N_FYN_F2990% H2O/10% D2O
solution50.2 mM [U-99% 15N] Monobody Binder, 1 mM Unlabeled FYN SH3 domain, 90% H2O/10% D2O15N_F29_FYN90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFYN SH3 domain[U-99% 13C; U-99% 15N]1
1 mMMonobody Binder[U-99% 13C; U-99% 15N]2
1 mMFYN SH3 domain[U-99% 15N; U-98% 2H]3
1.5 mMMonobody BinderUnlabeled3
0.2 mMFYN SH3 domain[U-99% 15N]4
1 mMMonobody BinderUnlabeled4
0.2 mMMonobody Binder[U-99% 15N]5
1 mMFYN SH3 domainUnlabeled5
Sample conditionsIonic strength: 300 mM / Label: conditions_1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
HADDOCKBonvinstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4 / Details: Docking with NMR restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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