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- PDB-7t1u: Crystal structure of a superbinder Src SH2 domain (sSrcF) in comp... -

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Basic information

Entry
Database: PDB / ID: 7t1u
TitleCrystal structure of a superbinder Src SH2 domain (sSrcF) in complex with a high affinity phosphopeptide
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • Synthetic phosphopeptide
KeywordsSIGNALING PROTEIN / Src Homology 2 (SH2) / rationally engineered / phosphotyrosine
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of telomere maintenance / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of telomere maintenance / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / negative regulation of focal adhesion assembly / positive regulation of integrin activation / positive regulation of protein processing / Activated NTRK2 signals through FYN / BMP receptor binding / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / Netrin mediated repulsion signals / negative regulation of neutrophil activation / focal adhesion assembly / connexin binding / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / regulation of vascular permeability / signal complex assembly / branching involved in mammary gland duct morphogenesis / positive regulation of small GTPase mediated signal transduction / Co-stimulation by CD28 / EPH-Ephrin signaling / positive regulation of podosome assembly / DCC mediated attractive signaling / positive regulation of lamellipodium morphogenesis / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / podosome / odontogenesis / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / Signaling by ALK / regulation of early endosome to late endosome transport / leukocyte migration / phospholipase activator activity / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / Co-inhibition by CTLA4 / p130Cas linkage to MAPK signaling for integrins / oogenesis / interleukin-6-mediated signaling pathway / Receptor Mediated Mitophagy / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / stimulatory C-type lectin receptor signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of cell-cell adhesion / forebrain development / uterus development / negative regulation of intrinsic apoptotic signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / Recycling pathway of L1 / RHOU GTPase cycle / regulation of heart rate by cardiac conduction / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / FCGR activation / positive regulation of epithelial cell migration / positive regulation of protein serine/threonine kinase activity / progesterone receptor signaling pathway / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / bone resorption / Nuclear signaling by ERBB4 / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / T cell costimulation / p38MAPK events / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / Integrin signaling / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / substrate adhesion-dependent cell spreading / Downstream signal transduction
Similarity search - Function
: / 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 / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMartyn, G.D. / Singer, A.U. / Manczyk, N. / 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 6, 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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
D: Synthetic phosphopeptide
E: Synthetic phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5548
Polymers27,2924
Non-polymers2624
Water32418
1
A: Proto-oncogene tyrosine-protein kinase Src
D: Synthetic phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7113
Polymers13,6462
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
E: Synthetic phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8425
Polymers13,6462
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.870, 35.890, 53.980
Angle α, β, γ (deg.)75.850, 74.770, 61.420
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 144 through 149 or (resid 150...
d_2ens_1(chain "B" and (resid 144 through 162 or (resid 163...
d_1ens_2chain "D"
d_2ens_2chain "E"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPROA1 - 28
d_12ens_1GLYTHRA30 - 105
d_21ens_1ALAPROB3 - 30
d_22ens_1GLYTHRB32 - 107
d_11ens_2GLUILEG1 - 7
d_21ens_2GLUILEH1 - 7

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999967432103, 0.00337916661485, -0.00732911772549), (0.0033815136602, -0.999994235275, 0.000307867414845), (-0.00732803513985, -0.000332640899956, -0.999973094264)3.4675225455, -4.62886312528, 13.8131355257
2given(0.996149533978, -0.0836404107651, -0.0262752286997), (-0.0833954171525, -0.99646343281, 0.0102874423418), (-0.0270427504911, -0.00805659723643, -0.999601811166)4.17199399965, -2.45161483377, 14.5666859665

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 12659.173 Da / Num. of mol.: 2 / Fragment: SH2 domain
Mutation: Residues 180 to 188 mutated from SETTKGAYC to GQSQPDYV and K206I (numbered as residue 205 in these coordinates)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Plasmid: PHH1028 / Details (production host): Nterm: His6x-TEVcleavage / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Protein/peptide Synthetic phosphopeptide


Mass: 986.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 80 uM Zinc Acetate, 12% PEG3350, 100 mM Sodium Acetate (pH 4.0), and 2% 1,3-butanediol
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: Aug 5, 2018 / 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: 2.6→51.57 Å / Num. obs: 5824 / % possible obs: 86.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 53.32 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 729 / CC1/2: 0.919 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5A

4f5a


Resolution: 2.65→51.57 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.2581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 547 9.99 %
Rwork0.2184 4929 -
obs0.2237 5476 85.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.06 Å2
Refinement stepCycle: LAST / Resolution: 2.65→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 4 18 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721826
X-RAY DIFFRACTIONf_angle_d1.03342488
X-RAY DIFFRACTIONf_chiral_restr0.0493271
X-RAY DIFFRACTIONf_plane_restr0.0069321
X-RAY DIFFRACTIONf_dihedral_angle_d16.7025639
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.910598560881
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.35268196615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.35261320.30561250X-RAY DIFFRACTION86.65
2.92-3.340.35661380.27991231X-RAY DIFFRACTION86.15
3.34-4.210.25211400.20791191X-RAY DIFFRACTION83.19
4.21-51.570.23451370.18291257X-RAY DIFFRACTION87.29

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