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- PDB-1shf: CRYSTAL STRUCTURE OF THE SH3 DOMAIN IN HUMAN FYN; COMPARISON OF T... -

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Entry
Database: PDB / ID: 1shf
TitleCRYSTAL STRUCTURE OF THE SH3 DOMAIN IN HUMAN FYN; COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF SH3 DOMAINS IN TYROSINE KINASES AND SPECTRIN
ComponentsFYN TYROSINE KINASE SH3 DOMAIN
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / cellular response to L-glutamate / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / cellular response to L-glutamate / heart process / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / Nef and signal transduction / feeding behavior / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / DCC mediated attractive signaling / Nephrin family interactions / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / CTLA4 inhibitory signaling / tau-protein kinase activity / phospholipase activator activity / leukocyte migration / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / cellular response to platelet-derived growth factor stimulus / cellular response to glycine / Dectin-2 family / glial cell projection / stimulatory C-type lectin receptor signaling pathway / phospholipase binding / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / response to amyloid-beta / alpha-tubulin binding / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / 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 / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of protein ubiquitination / negative regulation of inflammatory response to antigenic stimulus / Signaling by ERBB2 / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / 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 / actin filament / axon guidance / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / neuron migration / protein catabolic process / non-specific protein-tyrosine kinase / tau protein binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / non-membrane spanning protein tyrosine kinase activity / negative regulation of protein catabolic process / Signaling by SCF-KIT / positive regulation of neuron projection development / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport / Signaling by CSF1 (M-CSF) in myeloid cells / disordered domain specific binding / PIP3 activates AKT signaling
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. ...: / Fyn/Yrk, SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / 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)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsNoble, M. / Musacchio, A. / Saraste, M. / Wierenga, R.
CitationJournal: EMBO J. / Year: 1993
Title: Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.
Authors: Noble, M.E. / Musacchio, A. / Saraste, M. / Courtneidge, S.A. / Wierenga, R.K.
History
DepositionMay 19, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FYN TYROSINE KINASE SH3 DOMAIN
B: FYN TYROSINE KINASE SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)13,4772
Polymers13,4772
Non-polymers00
Water0
1
A: FYN TYROSINE KINASE SH3 DOMAIN
B: FYN TYROSINE KINASE SH3 DOMAIN

A: FYN TYROSINE KINASE SH3 DOMAIN
B: FYN TYROSINE KINASE SH3 DOMAIN


Theoretical massNumber of molelcules
Total (without water)26,9534
Polymers26,9534
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)73.700, 48.600, 43.000
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FYN TYROSINE KINASE SH3 DOMAIN


Mass: 6738.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P06241, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMDTT1drop
44 Msodium formate1reservoir
50.6 %beta-mercaptoethanol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 10190 / % possible obs: 86 % / Num. measured all: 37654 / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 0 956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.9
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5 Å / Num. reflection obs: 9808 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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