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- PDB-7a2l: Crystal structure of the Fyn SH3 domain mutant E129Q in space gro... -

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Basic information

Entry
Database: PDB / ID: 7a2l
TitleCrystal structure of the Fyn SH3 domain mutant E129Q in space group C21 at pH 4.0
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
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 / heart process / cellular response to L-glutamate / 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 / heart process / cellular response to L-glutamate / 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 / G protein-coupled glutamate receptor signaling pathway / 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 / feeding behavior / Nef and signal transduction / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / glial cell projection / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / Sema3A PAK dependent Axon repulsion / cellular response to glycine / alpha-tubulin binding / FCGR activation / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / 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 / regulation of peptidyl-tyrosine phosphorylation / forebrain development / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / 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 / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / protein catabolic process / modulation of chemical synaptic transmission / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport / Signaling by CSF1 (M-CSF) in myeloid cells / disordered domain specific 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 / SH3-like 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
FORMIC ACID / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
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 mutant E129Q in space group C21 at pH 4.0
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7045
Polymers13,5892
Non-polymers1153
Water79344
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9094
Polymers6,7941
Non-polymers1153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)6,7941
Polymers6,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.584, 45.896, 42.938
Angle α, β, γ (deg.)90.000, 97.120, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 85 through 93 or (resid 94...
21(chain B 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
11THRTHRTYRTYR(chain A and (resid 85 through 93 or (resid 94...AA85 - 933 - 11
12GLUGLUARGARG(chain A and (resid 85 through 93 or (resid 94...AA94 - 9612 - 14
13THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
14THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
15THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
16THRTHRVALVAL(chain A and (resid 85 through 93 or (resid 94...AA85 - 1413 - 59
21THRTHRTHRTHR(chain B and ((resid 85 and (name N or name...BB853
22GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
23GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
24GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 1411 - 59
25GLYGLYVALVAL(chain B and ((resid 85 and (name N or name...BB83 - 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: 6794.351 Da / Num. of mol.: 2 / Mutation: E129Q
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-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 3.5M sodium formate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→19.48 Å / Num. obs: 21066 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.052 / Rrim(I) all: 0.096 / Net I/σ(I): 7.1
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
1.9-1.943.20.90624217630.6840.6011.0911.399.7
8.91-19.482.90.093171090.9870.0620.1118.291

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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: 1.9→19.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 36.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1105 5.25 %
Rwork0.207 19961 -
obs0.2098 21066 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.56 Å2 / Biso mean: 52.5814 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 1.9→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 10 44 965
Biso mean--64.3 46.56 -
Num. residues----116
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A450X-RAY DIFFRACTION8.734TORSIONAL
12B450X-RAY DIFFRACTION8.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.990.38531360.34142430256693
1.99-2.090.3461470.27632458260595
2.09-2.220.32751430.27122481262496
2.22-2.390.32011510.24552449260095
2.39-2.630.31061260.28342526265297
2.63-3.010.33071360.24592530266697
3.01-3.790.24021420.19032536267898
3.79-19.480.19151240.14942551267597
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)
15.84-5.9338-0.04326.61451.45354.697-0.7005-0.5350.03880.49680.64290.2350.36330.16430.1650.23760.03680.01240.37350.00180.174721.79221.64913.4656
26.75020.6773-0.75593.96193.77173.8857-0.3485-0.2806-0.70830.23870.31350.19720.18280.3389-0.03170.34750.04130.07840.41980.01360.371423.5764-7.59647.2315
32.0881-0.96061.46418.44770.0162.2958-0.4490.23770.0336-0.47610.4751-0.6842-0.1920.69920.06210.3009-0.0081-0.01150.7171-0.13680.389829.73512.454910.0047
44.8451-4.45975.08218.4784-5.56765.3736-0.470.3791-0.2667-0.21150.3386-1.04390.31931.07820.01410.3216-0.00950.04560.5905-0.07560.396530.1935-0.33178.4699
57.5727-5.3137-2.95843.73552.42776.93390.7222-0.1579-1.22840.83710.7215-0.81712.19930.7331-1.25840.59450.155-0.0850.447-0.02120.596130.0712-6.197717.9752
68.8481-2.09220.78438.45773.39228.7319-0.17360.0503-0.21410.17120.2729-0.41510.04710.5198-0.09980.19670.0447-0.00870.37020.02570.238225.29472.71649.5055
75.94631.7518-0.66115.5583-1.77897.0855-0.127-0.7430.0762-0.0289-0.09030.42210.1187-0.0180.23760.27520.12890.01610.3626-0.00760.33939.710613.540413.434
87.9172-4.7686-2.78696.91171.64639.6142-0.03290.33280.2451-0.3594-0.2948-0.0608-1.0142-0.73450.43080.3390.0206-0.00610.3764-0.01160.299910.26518.48588.8564
99.6032-0.715-0.15456.97646.61516.9722-0.076-0.40650.1692-0.0238-0.16780.0853-0.0965-0.62610.2070.33040.07870.0250.37010.07240.201911.026715.38211.2338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 94 )A85 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 104 )A95 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 118 )A105 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 124 )A119 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 129 )A125 - 129
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 141 )A130 - 141
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 104 )B83 - 104
8X-RAY DIFFRACTION8chain 'B' and (resid 105 through 123 )B105 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 141 )B124 - 141

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