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- PDB-7t1k: Crystal structure of a superbinder Fes SH2 domain (sFes1) in comp... -

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Basic information

Entry
Database: PDB / ID: 7t1k
TitleCrystal structure of a superbinder Fes SH2 domain (sFes1) 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 / engineered / phage display
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / regulation of microvillus length / establishment or maintenance of apical/basal cell polarity / regulation of organelle assembly / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / microvillus assembly / positive regulation of myeloid cell differentiation ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / regulation of microvillus length / establishment or maintenance of apical/basal cell polarity / regulation of organelle assembly / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / microvillus assembly / positive regulation of myeloid cell differentiation / membrane to membrane docking / Netrin-1 signaling / establishment of centrosome localization / uropod / regulation of mast cell degranulation / astral microtubule organization / negative regulation of p38MAPK cascade / positive regulation of protein localization to early endosome / protein kinase A signaling / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical microtubule organization / cellular response to vitamin D / regulation of cell motility / filopodium assembly / CRMPs in Sema3A signaling / microtubule bundle formation / protein-containing complex localization / positive regulation of monocyte differentiation / positive regulation of multicellular organism growth / sphingosine-1-phosphate receptor signaling pathway / S100 protein binding / establishment of endothelial barrier / centrosome cycle / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / immunoglobulin receptor binding / negative regulation of interleukin-2 production / leukocyte cell-cell adhesion / negative regulation of T cell receptor signaling pathway / protein kinase A binding / microvillus membrane / cortical cytoskeleton / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / microvillus / Recycling pathway of L1 / brush border / regulation of cell differentiation / myoblast proliferation / actin filament bundle assembly / plasma membrane raft / Sema3A PAK dependent Axon repulsion / immunological synapse / cardiac muscle cell proliferation / regulation of cell adhesion / cell adhesion molecule binding / ruffle / positive regulation of microtubule polymerization / phosphatidylinositol binding / peptidyl-tyrosine phosphorylation / cellular response to cAMP / cell periphery / protein localization to plasma membrane / cell projection / actin filament / adherens junction / positive regulation of protein localization to plasma membrane / filopodium / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Signaling by SCF-KIT / positive regulation of neuron projection development / negative regulation of ERK1 and ERK2 cascade / receptor internalization / ruffle membrane / cytoplasmic side of plasma membrane / fibrillar center / chemotaxis / apical part of cell / positive regulation of protein catabolic process / disordered domain specific binding / actin filament binding / actin cytoskeleton / regulation of cell shape / regulation of cell population proliferation / actin binding / microtubule cytoskeleton / protein autophosphorylation / ATPase binding / actin cytoskeleton organization / cytoplasmic vesicle / protein tyrosine kinase activity / vesicle / basolateral plasma membrane / microtubule binding / cell adhesion / endosome / ciliary basal body / apical plasma membrane
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Fes/CIP4, and EFC/F-BAR homology domain ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
MALONATE ION / Tyrosine-protein kinase Fes/Fps / Ezrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,8138
Polymers12,4932
Non-polymers3206
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size exclusion chromatography, mass spectrometry, phosphopeptide pulldowns from K562 cell lysate
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-28 kcal/mol
Surface area6140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.080, 66.080, 58.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 11613.306 Da / Num. of mol.: 1 / Fragment: SH2 domain / Mutation: S485G, G487S, K488Q, Q489P, E490D
Source method: isolated from a genetically manipulated source
Details: Superbinder version of the Fes SH2 domain engineered using phage display
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pHH1028 / Details (production host): Ntermimus: 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.: 1 / Source method: obtained synthetically / Details: Fragment of Ezrin protein / Source: (synth.) Homo sapiens (human) / References: UniProt: P15311

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Non-polymers , 5 types, 123 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.4 M Sodium Malonate (pH 5.5) and 2% PEG300 / 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: Jun 9, 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: 1.25→58.89 Å / Num. obs: 40953 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 12.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Net I/σ(I): 10.2
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 11.2 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2021 / CC1/2: 0.463 / % possible all: 100

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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: 1.25→57.23 Å / SU ML: 0.1194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1781 1985 4.91 %
Rwork0.1517 38406 -
obs0.153 40391 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.56 Å2
Refinement stepCycle: LAST / Resolution: 1.25→57.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 18 117 1002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078936
X-RAY DIFFRACTIONf_angle_d1.08221276
X-RAY DIFFRACTIONf_chiral_restr0.0739138
X-RAY DIFFRACTIONf_plane_restr0.0089165
X-RAY DIFFRACTIONf_dihedral_angle_d9.348131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.30371370.28682728X-RAY DIFFRACTION99.83
1.28-1.320.28291440.2672728X-RAY DIFFRACTION99.86
1.32-1.350.23581460.22752715X-RAY DIFFRACTION99.97
1.35-1.40.251400.20922738X-RAY DIFFRACTION99.72
1.4-1.450.21291420.19962719X-RAY DIFFRACTION99.83
1.45-1.510.22791420.18832759X-RAY DIFFRACTION99.86
1.51-1.570.17511400.15142729X-RAY DIFFRACTION100
1.58-1.660.17681470.13782739X-RAY DIFFRACTION99.97
1.66-1.760.18081370.13122731X-RAY DIFFRACTION99.97
1.76-1.90.15931380.13182758X-RAY DIFFRACTION99.97
1.9-2.090.15491410.12042734X-RAY DIFFRACTION99.97
2.09-2.390.1581470.13072758X-RAY DIFFRACTION99.97
2.39-3.010.15311380.1422768X-RAY DIFFRACTION99.93
3.01-57.230.16841460.14522802X-RAY DIFFRACTION99.97

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