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- PDB-4znx: Crystal structure of the Fyn-SH3 domain in complex with the high ... -

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Basic information

Entry
Database: PDB / ID: 4znx
TitleCrystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12
Components
  • APP12
  • Tyrosine-protein kinase Fyn
KeywordsSIGNALING PROTEIN / beta shandwich
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 / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / 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 / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / activated T cell proliferation / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / 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 / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator 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 / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / glial cell projection / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / CD28 dependent PI3K/Akt signaling / 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 / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / T cell costimulation / Signaling by ERBB2 / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / learning / Cell surface interactions at the vascular wall / actin filament / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor binding / modulation of chemical synaptic transmission / protein catabolic process / Signaling by SCF-KIT / peptidyl-tyrosine phosphorylation / negative regulation of protein catabolic process / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / tau protein binding / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / cellular response to amyloid-beta / neuron migration / Signaling by CSF1 (M-CSF) in myeloid cells / calcium ion transport / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOBIO2012-39922-C02-02 Spain
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase.
Authors: Camara-Artigas, A. / Ortiz-Salmeron, E. / Andujar-Sanchez, M. / Bacarizo, J. / Martin-Garcia, J.M.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: APP12
F: APP12
G: APP12
H: APP12


Theoretical massNumber of molelcules
Total (without water)32,0398
Polymers32,0398
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-44 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.658, 76.664, 73.175
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number4
Space group name H-MP1211

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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: 6623.196 Da / Num. of mol.: 4 / Fragment: SH3 DOMAIN, UNP residues 84-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: PET3D / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Protein/peptide
APP12


Mass: 1386.667 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4 M sodium formate, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Number: 153807 / Rmerge(I) obs: 0.092 / D res high: 2.1 Å / D res low: 19.86 Å / Num. obs: 20052 / % possible obs: 98.2 / Rejects: 30
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.12.1610.6363.7
8.9119.8610.1126.8
ReflectionResolution: 2.1→19.86 Å / Num. obs: 20052 / % possible obs: 98.2 % / Redundancy: 7.7 % / Biso Wilson estimate: 42.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Net I/σ(I): 16.6 / Num. measured all: 153807 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.163.70.6363517613940.7850.35684.6
8.91-19.866.80.11251.217982630.9960.04491.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UA6

3ua6


Resolution: 2.1→19.858 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1978 5.11 %5
Rwork0.1795 36693 --
obs0.1817 38671 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.89 Å2 / Biso mean: 55.2822 Å2 / Biso min: 30.79 Å2
Refinement stepCycle: final / Resolution: 2.1→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 0 58 2120
Biso mean---47.93 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012127
X-RAY DIFFRACTIONf_angle_d1.1812915
X-RAY DIFFRACTIONf_chiral_restr0.053310
X-RAY DIFFRACTIONf_plane_restr0.006381
X-RAY DIFFRACTIONf_dihedral_angle_d12.228741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15250.4185880.30432146X-RAY DIFFRACTION79
2.1525-2.21060.31761280.28092373X-RAY DIFFRACTION88
2.2106-2.27560.28641210.25172630X-RAY DIFFRACTION96
2.2756-2.3490.26471180.2312652X-RAY DIFFRACTION99
2.349-2.43280.27011140.23092796X-RAY DIFFRACTION99
2.4328-2.530.27191390.22152626X-RAY DIFFRACTION99
2.53-2.64490.26061820.20682708X-RAY DIFFRACTION99
2.6449-2.7840.2591720.19882629X-RAY DIFFRACTION99
2.784-2.95790.2561460.19072714X-RAY DIFFRACTION100
2.9579-3.18540.23581710.18442697X-RAY DIFFRACTION99
3.1854-3.50440.22541540.15512678X-RAY DIFFRACTION100
3.5044-4.00780.16711530.1442709X-RAY DIFFRACTION100
4.0078-5.03580.17791590.13092638X-RAY DIFFRACTION99
5.0358-19.8580.22581330.20152697X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0359-0.02010.1043-0.0082-0.04320.33510.6942-0.66880.21060.9123-0.9045-0.6077-0.0294-0.354-0.01020.43820.005-0.0710.54950.11070.5987-16.6582-31.5803-39.6994
21.4780.70090.45961.631-0.95371.2609-0.204-0.1749-0.387-0.53760.11530.54570.3366-0.3227-0.00170.4216-0.0449-0.00860.59190.04050.6077-28.863-33.9385-49.7781
30.44760.00730.48220.2876-0.03590.479-0.2682-0.0893-0.48050.3541-0.26040.1470.8013-1.2431-0.0020.6394-0.07570.09160.5720.08480.632-26.7004-36.3618-44.3123
43.0191-0.52441.36092.25931.28881.60090.0405-0.0996-0.0904-0.3247-0.0119-0.49280.23930.1427-0.00040.41030.0250.03020.48420.02150.5329-16.3111-32.9466-48.5311
51.86211.49731.16962.3022-0.05261.32950.1078-0.2521-0.4011-0.16360.0112-0.76490.776-0.047-0.00010.51140.0367-0.00990.4530.03160.511-21.0605-33.6147-45.3386
60.685-0.4405-0.43020.52310.70011.34790.06070.10090.43530.1532-0.14070.498-0.766-0.0318-0.00010.4234-0.0542-0.0250.4826-0.03880.5174-24.2341-8.2799-38.8092
70.38290.6226-0.37480.9214-0.67850.82540.3507-0.6809-0.419-0.0649-0.21160.2656-0.02870.4462-0.00050.5753-0.06450.08350.6116-0.02990.5002-20.7849-17.4482-34.0244
80.89490.41030.11781.0524-0.50121.8470.0399-0.0732-0.2106-0.3595-0.18550.2505-0.3687-0.1978-0.00010.5207-0.07530.04190.5974-0.05670.5022-15.9529-8.9024-39.8815
90.95311.2014-0.88831.5465-0.97441.2009-0.0255-0.39570.05280.84030.15570.0212-0.04780.47410.00090.5514-0.0098-0.08130.559-0.05830.5463-15.43-11.3892-35.9884
100.1591-0.05280.06050.052-0.19670.9214-0.23890.00510.79870.48670.32790.8448-0.8290.14960.00270.5885-0.10530.02490.465-0.08330.5886-22.4516-7.295-43.5762
111.8892-0.1629-1.19552.6727-0.09891.9058-0.14020.01470.48340.21590.10860.2005-0.438-0.3027-0.00010.6780.0315-0.04830.55250.0370.5702-29.5859-1.0546-56.3277
120.7504-0.04210.15332.38830.68751.7640.4518-0.2049-0.3513-0.4419-0.2846-0.1608-0.49390.29530.00090.644-0.06250.02310.57880.0770.5355-22.8859-2.6104-61.9174
131.2731-1.8465-0.91142.60920.83152.65970.14840.04040.3742-0.0848-0.1607-0.3285-0.6802-0.0669-0.00010.6328-0.0209-0.06750.49510.04260.5233-25.0542-1.3281-60.3923
140.49280.34910.38480.44410.26670.50320.59970.7412-0.1713-0.0018-0.28130.02030.62490.62810.00090.4939-0.0393-0.00840.5503-0.08280.5683-26.9924-32.242-66.609
152.2302-0.510.91261.0668-0.30651.4961-0.02810.48680.2137-0.3375-0.25930.71-0.9824-0.08310.00010.6866-0.0109-0.12210.624-0.06140.6352-34.8794-21.2072-67.2036
162.4324-1.90430.61734.12342.25062.8331-0.02260.4852-0.0392-0.8417-0.04170.1674-0.10470.39820.00140.6825-0.0203-0.02780.529-0.04950.4607-26.3452-24.9196-68.7891
172.50370.66142.39862.74690.63912.2843-0.2471-0.12250.3127-0.2920.6176-0.28030.87450.5473-0.00210.4221-0.0020.01130.4336-0.00460.3989-24.2295-26.1836-56.0175
183.68381.38041.86914.51430.00683.24760.49060.30270.24990.2149-0.3515-1.104-0.33120.14020.01950.3832-0.0373-0.02270.4188-0.00070.4919-20.5685-20.4513-45.3693
190.1004-0.23480.06671.1151-1.11621.45890.13590.27380.3198-0.3071-0.16040.2638-0.2886-0.0137-0.00070.5721-0.0733-0.05750.51460.02990.4472-24.7456-9.2893-50.9646
201.4864-0.89841.1512.04240.54341.9548-0.3777-0.23370.4639-1.49070.31440.05960.2067-0.1137-0.00450.6033-0.0470.05620.4214-0.01360.4983-27.1003-15.133-60.9173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 89 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 99 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 107 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 124 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 141 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 94 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 104 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 105 through 118 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 134 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 141 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 86 through 104 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 105 through 118 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 119 through 141 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 85 through 89 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 90 through 107 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 108 through 141 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 10 )E0
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 10 )F0
19X-RAY DIFFRACTION19chain 'G' and (resid 1 through 9 )G0
20X-RAY DIFFRACTION20chain 'H' and (resid 1 through 10 )H0

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