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- PDB-7a2k: Crystal structure of the Fyn SH3 domain in space group P1 at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 7a2k
TitleCrystal structure of the Fyn SH3 domain in space group P1 at pH 7.5
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
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 / heart process / Activated NTRK2 signals through FYN / 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 / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / CD4 receptor binding / Nef and signal transduction / cellular response to L-glutamate / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / natural killer cell activation / negative regulation of dendritic spine maintenance / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / growth factor receptor binding / cellular response to peptide hormone stimulus / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / dendrite morphogenesis / peptide hormone receptor binding / CD8 receptor binding / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / glial cell projection / CD28 dependent PI3K/Akt signaling / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / alpha-tubulin binding / cellular response to transforming growth factor beta stimulus / postsynaptic density, intracellular component / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / phosphatidylinositol 3-kinase binding / phospholipase binding / GPVI-mediated activation cascade / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / negative regulation of protein ubiquitination / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / actin filament / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / Signaling by SCF-KIT / G protein-coupled receptor binding / positive regulation of neuron projection development / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / positive regulation of protein localization to nucleus / VEGFA-VEGFR2 Pathway / tau protein binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...: / Fyn/Yrk, SH3 domain / : / 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
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsP1 structure
AuthorsCamara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the Fyn SH3 domain in space group P1 at pH 7.5
Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Tyrosine-protein kinase Fyn
C: Tyrosine-protein kinase Fyn
D: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2738
Polymers27,1814
Non-polymers924
Water2,360131
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8182
Polymers6,7951
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8182
Polymers6,7951
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8182
Polymers6,7951
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8182
Polymers6,7951
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.811, 43.337, 43.346
Angle α, β, γ (deg.)65.270, 83.420, 83.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 85 through 95 or resid 97...
21(chain B and (resid 85 through 93 or (resid 94...
31(chain C and ((resid 85 and (name N or name...
41(chain D and ((resid 85 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA(chain A and (resid 85 through 95 or resid 97...AA85 - 953 - 13
12THRTHRPHEPHE(chain A and (resid 85 through 95 or resid 97...AA97 - 10915 - 27
13ILEILELEULEU(chain A and (resid 85 through 95 or resid 97...AA111 - 11229 - 30
14SERSERSERSER(chain A and (resid 85 through 95 or resid 97...AA11432
15GLYGLYALAALA(chain A and (resid 85 through 95 or resid 97...AA117 - 12235 - 40
16SERSERVALVAL(chain A and (resid 85 through 95 or resid 97...AA124 - 14142 - 59
21THRTHRTYRTYR(chain B and (resid 85 through 93 or (resid 94...BB85 - 933 - 11
22GLUGLUALAALA(chain B and (resid 85 through 93 or (resid 94...BB94 - 9512 - 13
23THRTHRASPASP(chain B and (resid 85 through 93 or (resid 94...BB85 - 1423 - 60
24THRTHRASPASP(chain B and (resid 85 through 93 or (resid 94...BB85 - 1423 - 60
25THRTHRASPASP(chain B and (resid 85 through 93 or (resid 94...BB85 - 1423 - 60
26THRTHRASPASP(chain B and (resid 85 through 93 or (resid 94...BB85 - 1423 - 60
31THRTHRTHRTHR(chain C and ((resid 85 and (name N or name...CC853
32VALVALVALVAL(chain C and ((resid 85 and (name N or name...CC84 - 1412 - 59
33VALVALVALVAL(chain C and ((resid 85 and (name N or name...CC84 - 1412 - 59
34VALVALVALVAL(chain C and ((resid 85 and (name N or name...CC84 - 1412 - 59
35VALVALVALVAL(chain C and ((resid 85 and (name N or name...CC84 - 1412 - 59
41THRTHRTHRTHR(chain D and ((resid 85 and (name N or name...DD853
42GLYGLYVALVAL(chain D and ((resid 85 and (name N or name...DD83 - 1411 - 59
43GLYGLYVALVAL(chain D and ((resid 85 and (name N or name...DD83 - 1411 - 59
44GLYGLYVALVAL(chain D and ((resid 85 and (name N or name...DD83 - 1411 - 59
45GLYGLYVALVAL(chain D and ((resid 85 and (name N or name...DD83 - 1411 - 59

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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: 6795.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.5M sodium formate, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.5→19.49 Å / Num. obs: 66932 / % possible obs: 93.3 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.028 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.531.80.398375620660.8840.3980.5631.393.4
8.22-19.491.90.0144342310.9990.0140.0217.785.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 1.5→19.49 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.53 / Phase error: 36.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 3551 5.31 %
Rwork0.2019 63381 -
obs0.2038 66932 74.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.96 Å2 / Biso mean: 44.1676 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: final / Resolution: 1.5→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 4 131 1990
Biso mean--69.48 41.59 -
Num. residues----233
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A854X-RAY DIFFRACTION9.673TORSIONAL
12B854X-RAY DIFFRACTION9.673TORSIONAL
13C854X-RAY DIFFRACTION9.673TORSIONAL
14D854X-RAY DIFFRACTION9.673TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.32181220.33972314243668
1.52-1.540.42471420.31832353249569
1.54-1.570.3141390.30062316245570
1.57-1.590.36861230.29572498262172
1.59-1.620.28861140.28892405251971
1.62-1.640.38851360.28462483261973
1.64-1.670.27331490.27782495264474
1.67-1.710.32661420.26722432257472
1.71-1.740.35541130.2772594270775
1.74-1.780.35851530.26492598275177
1.78-1.820.33191300.26412578270876
1.82-1.870.26271290.26092636276575
1.87-1.920.31911490.24382434258373
1.92-1.970.25331830.24062560274374
1.97-2.040.25881450.23282481262674
2.04-2.110.28481180.21062523264175
2.11-2.190.24761630.21142713287678
2.19-2.290.31681210.2172670279178
2.29-2.410.24831570.21282581273876
2.41-2.560.32551850.2422593277877
2.56-2.760.27041140.24192589270377
2.76-3.040.21281570.22372747290480
3.04-3.470.21931620.18782430259273
3.48-4.370.1941550.14042604275976
4.37-19.490.16651500.16692754290481

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