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- PDB-7t1l: Crystal structure of a superbinder Fes SH2 domain (sFesS) in comp... -

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Basic information

Entry
Database: PDB / ID: 7t1l
TitleCrystal structure of a superbinder Fes SH2 domain (sFesS) in complex with a high affinity phosphopeptide
Components
  • Synthetic phosphotyrosine-containing Ezrin-derived peptide
  • Tyrosine-protein kinase Fes/Fps
KeywordsSIGNALING PROTEIN / Src Homology 2 (SH2) / superbinder / rational engineering
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / negative regulation of p38MAPK cascade / Netrin-1 signaling / cortical microtubule organization / uropod / regulation of mast cell degranulation / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to vitamin D / positive regulation of multicellular organism growth / filopodium assembly / CRMPs in Sema3A signaling / protein-containing complex localization / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / sphingosine-1-phosphate receptor signaling pathway / establishment of endothelial barrier / S100 protein binding / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / centrosome cycle / myoblast proliferation / protein kinase A binding / cardiac muscle cell proliferation / negative regulation of interleukin-2 production / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / cortical cytoskeleton / regulation of cell differentiation / protein kinase A regulatory subunit binding / Recycling pathway of L1 / protein kinase A catalytic subunit binding / plasma membrane raft / microvillus / brush border / actin filament bundle assembly / Sema3A PAK dependent Axon repulsion / immunological synapse / regulation of cell adhesion / immunoglobulin receptor binding / cellular response to cAMP / positive regulation of microtubule polymerization / cell adhesion molecule binding / ruffle / protein kinase A signaling / phosphatidylinositol binding / ciliary basal body / filopodium / cell projection / protein localization to plasma membrane / cell periphery / actin filament / positive regulation of protein localization to plasma membrane / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / receptor internalization / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / fibrillar center / ruffle membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of protein catabolic process / chemotaxis / microtubule cytoskeleton / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / regulation of cell population proliferation / regulation of cell shape / ATPase binding / cytoplasmic vesicle / actin cytoskeleton organization / microtubule binding / basolateral plasma membrane / protein tyrosine kinase activity / vesicle / protein autophosphorylation / cell adhesion / endosome / cadherin binding
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Fes/CIP4, and EFC/F-BAR homology domain ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / AH/BAR domain superfamily / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / 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 Fes/Fps / Ezrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMartyn, G.D. / Singer, A.U. / Veggiani, G. / Kurinov, I. / Sicheri, F. / Sidhu, S.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93684 United States
Canadian Institutes of Health Research (CIHR)FDN-143277 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Engineered SH2 Domains for Targeted Phosphoproteomics.
Authors: Martyn, G.D. / Veggiani, G. / Kusebauch, U. / Morrone, S.R. / Yates, B.P. / Singer, A.U. / Tong, J. / Manczyk, N. / Gish, G. / Sun, Z. / Kurinov, I. / Sicheri, F. / Moran, M.F. / Moritz, R.L. / Sidhu, S.S.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fes/Fps
B: Tyrosine-protein kinase Fes/Fps
C: Synthetic phosphotyrosine-containing Ezrin-derived peptide
D: Synthetic phosphotyrosine-containing Ezrin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2226
Polymers24,1644
Non-polymers582
Water3,261181
1
A: Tyrosine-protein kinase Fes/Fps
C: Synthetic phosphotyrosine-containing Ezrin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1053
Polymers12,0822
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-29 kcal/mol
Surface area5990 Å2
MethodPISA
2
B: Tyrosine-protein kinase Fes/Fps
D: Synthetic phosphotyrosine-containing Ezrin-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1173
Polymers12,0822
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-7 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.240, 60.660, 61.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tyrosine-protein kinase Fes/Fps / Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c- ...Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c-Fps / p93c-fes


Mass: 11201.869 Da / Num. of mol.: 2 / Fragment: SH2 domain
Mutation: Residues 486 to 492 mutated from QGKQEYV to ETVKGAYA, and I505L (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pHH1028 / Details (production host): Nterm: His6x-TEVcleavage / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07332, non-specific protein-tyrosine kinase
#2: Protein/peptide Synthetic phosphotyrosine-containing Ezrin-derived peptide


Mass: 879.888 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15311
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3 M Sodium Citrate Tribasic Dihydrate and 100 mM Bis-Tris Propane (pH=8.5)
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2019 / Details: mirrors
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→43.32 Å / Num. obs: 45098 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.758 / Num. unique obs: 2269 / CC1/2: 0.723 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BKB

3bkb


Resolution: 1.35→43.32 Å / SU ML: 0.1474 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 1804 4.47 %
Rwork0.164 38509 -
obs0.1655 40313 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.59 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 2 181 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921741
X-RAY DIFFRACTIONf_angle_d1.16592390
X-RAY DIFFRACTIONf_chiral_restr0.0817268
X-RAY DIFFRACTIONf_plane_restr0.0096309
X-RAY DIFFRACTIONf_dihedral_angle_d14.9635626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.390.28781410.21862881X-RAY DIFFRACTION98.86
1.39-1.430.26711340.19952908X-RAY DIFFRACTION98.35
1.43-1.470.22631330.18212878X-RAY DIFFRACTION97.86
1.47-1.530.24371320.16872930X-RAY DIFFRACTION99.48
1.53-1.590.22821430.15832918X-RAY DIFFRACTION99.22
1.59-1.660.17521370.15282939X-RAY DIFFRACTION99.74
1.66-1.750.20511310.15072949X-RAY DIFFRACTION99.64
1.75-1.860.20971390.14772952X-RAY DIFFRACTION99.61
1.86-20.19341460.15742959X-RAY DIFFRACTION99.2
2-2.20.17821380.15152979X-RAY DIFFRACTION99.78
2.2-2.520.19111390.15913004X-RAY DIFFRACTION100
2.52-3.170.17651420.183040X-RAY DIFFRACTION100
3.17-43.320.20091490.16273172X-RAY DIFFRACTION99.73

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