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- PDB-6sm5: MbC/SHP1-C-SH2 complex -

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Basic information

Entry
Database: PDB / ID: 6sm5
TitleMbC/SHP1-C-SH2 complex
Components
  • MbC (monobody targeting SHP1-C-SH2)
  • Tyrosine-protein phosphatase non-receptor type 6
KeywordsBIOSYNTHETIC PROTEIN / Complex / inhibitor / phosphatase / monobody
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / epididymis development / CD27 signaling pathway / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / Co-inhibition by BTLA ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / epididymis development / CD27 signaling pathway / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / Co-inhibition by BTLA / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of neutrophil activation / CD22 mediated BCR regulation / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Signal regulatory protein family interactions / platelet formation / Regulation of KIT signaling / megakaryocyte development / Signaling by ALK / negative regulation of T cell receptor signaling pathway / natural killer cell mediated cytotoxicity / Platelet sensitization by LDL / regulation of type I interferon-mediated signaling pathway / PECAM1 interactions / regulation of G1/S transition of mitotic cell cycle / negative regulation of interleukin-6 production / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / negative regulation of tumor necrosis factor production / Interleukin-3, Interleukin-5 and GM-CSF signaling / Co-inhibition by PD-1 / Interleukin receptor SHC signaling / negative regulation of MAPK cascade / Regulation of IFNG signaling / hematopoietic progenitor cell differentiation / Growth hormone receptor signaling / regulation of ERK1 and ERK2 cascade / T cell proliferation / Nuclear events stimulated by ALK signaling in cancer / protein dephosphorylation / GPVI-mediated activation cascade / cell adhesion molecule binding / negative regulation of T cell proliferation / T cell costimulation / phosphotyrosine residue binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / SH2 domain binding / negative regulation of innate immune response / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / T cell activation / negative regulation of angiogenesis / B cell receptor signaling pathway / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / SH3 domain binding / platelet aggregation / specific granule lumen / Interferon gamma signaling / Interferon alpha/beta signaling / MAPK cascade / tertiary granule lumen / cell-cell junction / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMann, G. / Hantschel, O.
Funding support1items
OrganizationGrant numberCountry
European Research Council
CitationJournal: To Be Published
Title: MbC/SHP1-C-SH2 complex
Authors: Hantschel, O.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
B: MbC (monobody targeting SHP1-C-SH2)


Theoretical massNumber of molelcules
Total (without water)23,2652
Polymers23,2652
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-5 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.898, 63.820, 73.101
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 phosphatase non-receptor type 6 / Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / ...Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / Protein-tyrosine phosphatase SHP-1 / SH-PTP1


Mass: 13252.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN6, HCP, PTP1C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Antibody MbC (monobody targeting SHP1-C-SH2)


Mass: 10012.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic, 0.1 M bistros propane 8.4 and 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→48.1 Å / Num. obs: 10640 / % possible obs: 92 % / Redundancy: 2.11 % / Biso Wilson estimate: 39.5181160384 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.14 / Net I/σ(I): 7.09
Reflection shellResolution: 2.75→2.9 Å / Mean I/σ(I) obs: 1.73 / Num. unique obs: 1726 / CC1/2: 0.688 / Rrim(I) all: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jeg

4jeg


Resolution: 2.75→48.1 Å / SU ML: 0.46847011608 / Cross valid method: FREE R-VALUE / σ(F): 1.34188609808 / Phase error: 27.7366742674
RfactorNum. reflection% reflection
Rfree0.276452644706 1064 10.0282752121 %
Rwork0.219127249237 --
obs0.224949000386 10610 92.3090307987 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.9141762171 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 0 21 1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003160712249761579
X-RAY DIFFRACTIONf_angle_d0.618022296242154
X-RAY DIFFRACTIONf_chiral_restr0.0444694247405238
X-RAY DIFFRACTIONf_plane_restr0.0055401821697272
X-RAY DIFFRACTIONf_dihedral_angle_d3.18146150515913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.87540.4247490945241330.3128159367571218X-RAY DIFFRACTION93.4301521438
2.8754-3.02690.3419034043531390.2666071185311224X-RAY DIFFRACTION94.2600276625
3.0269-3.21650.3438096635421310.2485015744391206X-RAY DIFFRACTION93.3659217877
3.2165-3.46480.3045008098091320.2378814371461182X-RAY DIFFRACTION91.504178273
3.4648-3.81340.2626842867141250.2054746713211132X-RAY DIFFRACTION87.9020979021
3.8134-4.36490.243831958411350.1814512726331218X-RAY DIFFRACTION94.5492662474
4.3649-5.4980.1955843768231350.1798808351051205X-RAY DIFFRACTION92.9264909847
5.498-48.10.297126604831340.2341385865061161X-RAY DIFFRACTION90.4961565339

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