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- PDB-4u1p: Human Fyn-SH2 domain in complex with a synthetic high-affinity ph... -

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Basic information

Entry
Database: PDB / ID: 4u1p
TitleHuman Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide
Components
  • Middle T antigen
  • Tyrosine-protein kinase Fyn
KeywordsTRANSFERASE / SH2 domain / protein peptide interactions / allostery / tyrosine phosphorylation / Fyn / kinase
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 / 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 / host cell 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 / 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
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / : / Fyn/Yrk, SH3 domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / : / Fyn/Yrk, SH3 domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Middle T antigen / Middle T antigen / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
Hamster polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGarcia-Pino, A. / Huculeci, R. / Lenaerts, T. / van Nuland, N.A.J.
CitationJournal: To Be Published
Title: Human Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide
Authors: Garcia-Pino, A. / Huculeci, R. / Lenaerts, T. / van Nuland, N.A.J.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Source and taxonomy / Category: pdbx_entity_src_syn / pdbx_related_exp_data_set / Item: _pdbx_entity_src_syn.ncbi_taxonomy_id
Revision 1.2Dec 20, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn_type.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: Middle T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1484
Polymers15,5962
Non-polymers1,5532
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
  • DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-18 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.248, 39.248, 145.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 14122.016 Da / Num. of mol.: 1 / Fragment: Human Fyn-SH2 domain, RESIDUES 148-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Protein/peptide Middle T antigen


Mass: 1473.515 Da / Num. of mol.: 1 / Fragment: RESIDUES 320-330 / Source method: obtained synthetically / Source: (synth.) Hamster polyomavirus / References: UniProt: K0F5T5, UniProt: P03079*PLUS
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MOPS/Na HEPES pH 7.5, 0.12 M monosaccharide mixture, PEG 1000, 12.5%(w/v) PEG 3350 and 12.5%(v/v) MPD
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.4→23.34 Å / Num. obs: 23359 / % possible obs: 99.93 % / Redundancy: 14.7 % / Net I/σ(I): 24.43
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 7.73 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G83

1g83


Resolution: 1.4→23 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 1200 5.14 %Random selection
Rwork0.1511 ---
obs0.153 23343 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 12 185 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011008
X-RAY DIFFRACTIONf_angle_d1.3011363
X-RAY DIFFRACTIONf_dihedral_angle_d12.822390
X-RAY DIFFRACTIONf_chiral_restr0.052137
X-RAY DIFFRACTIONf_plane_restr0.007176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4003-1.45640.19271410.17392390X-RAY DIFFRACTION100
1.4564-1.52260.20031190.16732390X-RAY DIFFRACTION100
1.5226-1.60290.17581350.14942413X-RAY DIFFRACTION100
1.6029-1.70330.17511320.14642427X-RAY DIFFRACTION100
1.7033-1.83480.18171410.14542415X-RAY DIFFRACTION100
1.8348-2.01930.19031380.14852438X-RAY DIFFRACTION100
2.0193-2.31130.16241260.14922503X-RAY DIFFRACTION100
2.3113-2.91110.2031340.16612485X-RAY DIFFRACTION100
2.9111-23.34770.19231340.14352682X-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)
18.9039-4.2283-7.883123.07927.0241-0.2299-1.1535-0.24480.6769-0.0093-0.0879-0.35130.98430.24020.3822-0.0946-0.1390.31430.10160.233533.29196.09544.4178
23.78070.9816-0.36782.1655-0.55530.4630.0590.2390.3895-0.1121-0.02520.1357-0.0549-0.0798-0.04430.11420.0157-0.00980.15740.03580.117314.49918.254855.8889
32.7842-0.1697-0.33552.8024-0.12382.480.0894-0.1972-0.04240.1945-0.07550.060.0066-0.0638-0.01930.06960.00130.00220.1040.00370.069311.34271.974962.6766
45.45330.1574-0.49861.38460.3391.27420.0481-0.1016-0.1149-0.02230.0081-0.15650.02480.1225-0.05160.07670.0033-0.00730.09340.02060.092524.5067-1.050961.309
54.6661-4.38721.32186.6682-1.95910.8433-0.2286-0.5435-0.19060.73760.29050.0642-0.16940.0279-0.09180.20110.0197-0.00440.1910.03170.136520.2479-1.260472.2912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:9)
2X-RAY DIFFRACTION2(chain A and resid 10:37)
3X-RAY DIFFRACTION3(chain A and resid 38:71)
4X-RAY DIFFRACTION4(chain A and resid 72:112)
5X-RAY DIFFRACTION5(chain B and resid 1:11)

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