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- PDB-4je4: Crystal Structure of Monobody NSa1/SHP2 N-SH2 Domain Complex -

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Basic information

Entry
Database: PDB / ID: 4je4
TitleCrystal Structure of Monobody NSa1/SHP2 N-SH2 Domain Complex
Components
  • Monobody NSa1
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsSignaling protein/protein binding / engineered binding protein / SHP2 SH2-monobody complex / Phosphatase / Phosphotyrosine Binding / Phosphorylation / Signaling protein-protein binding complex
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / genitalia development / peptidase activator activity / atrioventricular canal development / fibrinogen complex / negative regulation of cell adhesion mediated by integrin / peptide cross-linking / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / positive regulation of hormone secretion / negative regulation of neutrophil activation / integrin activation / ALK mutants bind TKIs / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / cell-substrate junction assembly / Signaling by Leptin / hormone metabolic process / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / proteoglycan binding / face morphogenesis / Signal regulatory protein family interactions / ERBB signaling pathway / platelet formation / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / triglyceride metabolic process / organ growth / megakaryocyte development / negative regulation of type I interferon production / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Syndecan interactions / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / p130Cas linkage to MAPK signaling for integrins / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / regulation of cell adhesion mediated by integrin / platelet-derived growth factor receptor signaling pathway / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / positive regulation of intracellular signal transduction / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / basement membrane / RET signaling / Regulation of IFNA/IFNB signaling / Non-integrin membrane-ECM interactions / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / positive regulation of insulin receptor signaling pathway / ECM proteoglycans / GAB1 signalosome / Integrin cell surface interactions / ephrin receptor signaling pathway / Activated NTRK2 signals through FRS2 and FRS3 / endothelial cell migration / positive regulation of axon extension / regulation of protein-containing complex assembly / Regulation of IFNG signaling / regulation of ERK1 and ERK2 cascade / non-membrane spanning protein tyrosine phosphatase activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF)
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Protein-tyrosine phosphatase, non-receptor type-6, -11 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / SH2 domain / SHC Adaptor Protein / 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 / Kringle-like fold / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / SH2 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fibronectin / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSha, F. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains.
Authors: Sha, F. / Gencer, E.B. / Georgeon, S. / Koide, A. / Yasui, N. / Koide, S. / Hantschel, O.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Mar 12, 2014Group: Structure summary
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 11
B: Monobody NSa1


Theoretical massNumber of molelcules
Total (without water)22,2342
Polymers22,2342
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.581, 69.098, 84.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11 / Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP- ...Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP-2 / Shp2 / SH-PTP3


Mass: 12104.635 Da / Num. of mol.: 1 / Fragment: N-terminal SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTP2C, PTPN11, SHPTP2 / Plasmid: pHBT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06124
#2: Protein Monobody NSa1


Mass: 10129.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHFT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium Chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.31→34.55 Å / Num. all: 8458 / Num. obs: 8427 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.31→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5 / Num. unique all: 1181 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→34.55 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8243 / SU ML: 0.18 / σ(F): 1.38 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 314 4.53 %random
Rwork0.204 ---
obs0.2063 6926 82.81 %-
all-8427 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.793 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 54.32 Å2 / Biso mean: 19.2185 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.0058 Å2-0 Å2-0 Å2
2---0.9718 Å20 Å2
3---0.9776 Å2
Refinement stepCycle: LAST / Resolution: 2.31→34.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 0 85 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031573
X-RAY DIFFRACTIONf_angle_d0.7682145
X-RAY DIFFRACTIONf_chiral_restr0.051234
X-RAY DIFFRACTIONf_plane_restr0.004272
X-RAY DIFFRACTIONf_dihedral_angle_d12.294558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.90540.28151160.21782785290171
2.9054-34.55290.24591980.19863827402594

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