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- PDB-3tl0: Structure of SHP2 N-SH2 domain in complex with RLNpYAQLWHR peptide -

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Basic information

Entry
Database: PDB / ID: 3tl0
TitleStructure of SHP2 N-SH2 domain in complex with RLNpYAQLWHR peptide
Components
  • RLNpYAQLWHR peptide
  • Tyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE/Peptide / SH2 domain / Protein-protein interactions / phosphorylated tyrosine / HYDROLASE-Peptide complex
Function / homology
Function and homology information


negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / positive regulation of hormone secretion / negative regulation of neutrophil activation / regulation of protein export from nucleus / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / Interleukin-37 signaling / Signaling by Leptin / hormone metabolic process / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / Signal regulatory protein family interactions / face morphogenesis / ERBB signaling pathway / platelet formation / triglyceride metabolic process / megakaryocyte development / organ growth / negative regulation of type I interferon production / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / peptide hormone receptor binding / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / 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 / inner ear development / Bergmann glial cell differentiation / positive regulation of intracellular signal transduction / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / RET signaling / Regulation of IFNA/IFNB signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / Activated NTRK2 signals through FRS2 and FRS3 / regulation of protein-containing complex assembly / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNG signaling / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / Signaling by FLT3 ITD and TKD mutants / negative regulation of T cell proliferation / T cell costimulation / FRS-mediated FGFR2 signaling / hormone-mediated signaling pathway / cell adhesion molecule binding / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / FLT3 Signaling / protein-tyrosine-phosphatase / homeostasis of number of cells within a tissue / axonogenesis / Downstream signal transduction / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / DNA damage checkpoint signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / integrin-mediated signaling pathway / positive regulation of D-glucose import / insulin receptor binding / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / negative regulation of insulin secretion / Spry regulation of FGF signaling
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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, non-receptor type-6, -11 / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhang, Y. / Zhang, J. / Yuan, C. / Hard, R.L. / Park, I.H. / Li, C. / Bell, C.E. / Pei, D.
CitationJournal: Biochemistry / Year: 2011
Title: Simultaneous binding of two peptidyl ligands by a SRC homology 2 domain.
Authors: Zhang, Y. / Zhang, J. / Yuan, C. / Hard, R.L. / Park, I.H. / Li, C. / Bell, C. / Pei, D.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: RLNpYAQLWHR peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8243
Polymers13,7282
Non-polymers961
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-24 kcal/mol
Surface area5670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.749, 62.749, 75.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 12288.744 Da / Num. of mol.: 1 / Fragment: N-terminal SH2 domain, (UNP residues 1-106)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide RLNpYAQLWHR peptide


Mass: 1439.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide was synthesized with standard Fmoc.HBTU chemistry
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 0.1 M bis-Tris, 0.2 M Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Mar 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→48.2 Å / Num. obs: 9943 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 46.5
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 6.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPof CCP4phasing
REFMAC5.5.0100refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AYD

1ayd


Resolution: 2.05→24.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.682 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23358 467 4.8 %RANDOM
Rwork0.1927 ---
obs0.19448 9354 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 5 23 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021855
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9651165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60324.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19415126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.902154
X-RAY DIFFRACTIONr_chiral_restr0.1660.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021666
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5251.5523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7212830
X-RAY DIFFRACTIONr_scbond_it3.7773332
X-RAY DIFFRACTIONr_scangle_it5.9824.5335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 26 -
Rwork0.212 691 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
120.7418-1.613-0.01620.97161.73829.2798-0.4294-0.0325-0.04070.60720.6326-0.23010.50290.6678-0.20320.22950.0386-0.03160.2078-0.06150.202225.9885.02526.377
25.25338.8569-0.758316.85951.17621.1772-0.188-0.108-0.7102-0.62760.4011-0.8129-0.35190.4226-0.21310.2336-0.10920.06070.2587-0.07110.163424.31.86214.97
30.64341.5573-0.05695.38470.95331.4641-0.36220.0916-0.1799-0.52680.215-0.023-0.39220.21820.14720.3045-0.0751-0.03650.1633-0.02280.12519.5348.37118.812
4-0.59871.4346-0.68234.0498-0.04361.3349-0.0873-0.04570.1284-0.43370.17820.0332-0.0276-0.013-0.09090.2251-0.0274-0.05380.1270.00130.204719.79920.54627.06
51.435-1.42122.12496.5793-2.1283.2902-0.0675-0.0810.0958-0.02860.02670.3196-0.02320.02770.04080.17990.0051-0.04120.1641-0.02010.1917.86116.1233.836
67.89454.0859-0.56136.93621.04261.74260.0458-0.23920.09650.0944-0.28570.28840.18170.0320.240.1829-0.035-0.03020.1812-0.00850.174812.4939.91331.955
73.3869-5.16180.42216.1563-19.72658.8933-0.2297-0.54340.9901-1.70610.31070.42992.2294-2.1635-0.0810.2781-0.1007-0.28630.0143-0.06930.5746.98812.03824.243
83.5417-6.28055.4399.44886.998916.1165-0.1909-0.56310.0178-0.6099-0.4362-0.0443-0.6283-0.8830.62720.180.0409-0.23940.27180.22940.4165.22413.02117.753
97.82625.4551-2.97385.1421-0.70225.8253-0.1837-0.2229-0.42170.19720.09110.4030.01550.29640.09260.192-0.0045-0.0080.1151-0.02280.184314.9291.25525.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 9
2X-RAY DIFFRACTION2A10 - 23
3X-RAY DIFFRACTION3A24 - 53
4X-RAY DIFFRACTION4A54 - 68
5X-RAY DIFFRACTION5A69 - 76
6X-RAY DIFFRACTION6A77 - 84
7X-RAY DIFFRACTION7A85 - 90
8X-RAY DIFFRACTION8A91 - 96
9X-RAY DIFFRACTION9A97 - 103

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