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- PDB-3ua6: Crystal Structure of the Human Fyn SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3ua6
TitleCrystal Structure of the Human Fyn SH3 domain
ComponentsTyrosine-protein kinase Fyn
KeywordsTRANSFERASE / beta barrel
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 / CRMPs in Sema3A signaling / G protein-coupled glutamate receptor signaling pathway / FLT3 signaling through SRC family kinases / cellular response to L-glutamate / activated T cell proliferation / positive regulation of protein localization to membrane / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / CD4 receptor binding / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / DCC mediated attractive signaling / natural killer cell activation / EPH-Ephrin signaling / Ephrin signaling / CD28 dependent Vav1 pathway / dendritic spine maintenance / 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 / 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 / alpha-tubulin binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / postsynaptic density, intracellular component / cellular response to transforming growth factor beta stimulus / forebrain development / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / phospholipase binding / T cell receptor binding / phosphatidylinositol 3-kinase binding / GPVI-mediated activation cascade / T cell costimulation / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / 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 / Regulation of signaling by CBL / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Cell surface interactions at the vascular wall / learning / actin filament / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / protein catabolic process / peptidyl-tyrosine phosphorylation / G protein-coupled receptor binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / positive regulation of neuron projection development / Signaling by CSF1 (M-CSF) in myeloid cells / tau protein binding / positive regulation of protein localization to nucleus
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 / Src homology 3 domains ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / 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 / 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
FORMIC ACID / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCamara-Artigas, A. / Martin-Garcia, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The promiscuous binding of the Fyn SH3 domain to a peptide from the NS5A protein.
Authors: Martin-Garcia, J.M. / Luque, I. / Ruiz-Sanz, J. / Camara-Artigas, A.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,87313
Polymers14,3442
Non-polymers52911
Water1,35175
1
A: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,63210
Polymers7,1721
Non-polymers4609
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2413
Polymers7,1721
Non-polymers692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.293, 47.074, 42.467
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASNASN2AA85 - 1136 - 34
21THRTHRASNASN2BB85 - 1136 - 34
12ASPASPPROPRO4AA118 - 14039 - 61
22ASPASPPROPRO4BB118 - 14039 - 61

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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: 7171.764 Da / Num. of mol.: 2 / Fragment: SH3 domain (UNP residues 81-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5.5 M sodium formate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Microfocus (Montel Optics) / Detector: CCD / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→41.998 Å / Num. all: 12182 / Num. obs: 11459 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.0274 / Rsym value: 0.0274 / Net I/σ(I): 21.66
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 0.87 % / Rmerge(I) obs: 0.1511 / Mean I/σ(I) obs: 3.78 / Num. unique all: 1109 / Rsym value: 0.1511 / % possible all: 72.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.02 Å42 Å
Translation2.02 Å42 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
APEXdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHF

1shf


Resolution: 1.85→19.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.052 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 544 4.8 %RANDOM
Rwork0.177 ---
all0.1801 12170 --
obs0.1801 11447 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.82 Å2 / Biso mean: 25.454 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.06 Å2
2--0.53 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 33 75 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221018
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9471377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36524.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3815151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.186155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021795
X-RAY DIFFRACTIONr_mcbond_it2.0061.5603
X-RAY DIFFRACTIONr_mcangle_it2.9332953
X-RAY DIFFRACTIONr_scbond_it4.3543415
X-RAY DIFFRACTIONr_scangle_it6.7314.5422
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
114TIGHT POSITIONAL0.50.05
293MEDIUM POSITIONAL0.760.5
114TIGHT THERMAL1.790.5
293MEDIUM THERMAL2.192
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 25 -
Rwork0.188 454 -
all-479 -
obs--54.06 %
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)
12.8237-0.6960.21981.5698-0.4343.7608-0.00250.08570.04760.01510.0271-0.02150.01780.1312-0.02470.01480.012-0.00270.0245-0.01560.0284-7.656-0.41-10.494
22.2479-1.4578-0.18252.09040.57763.3265-0.0664-0.00520.0465-0.0101-0.05520.1065-0.20140.02140.12170.04510.0169-0.00760.02070.00470.0285-22.83215.502-9.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A85 - 141
2X-RAY DIFFRACTION2B83 - 142

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