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- PDB-6roy: Structure of the N-SH2 domain of the human tyrosine-protein phosp... -

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Basic information

Entry
Database: PDB / ID: 6roy
TitleStructure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif
Components
  • Tyrosine-protein phosphatase non-receptor type 11
  • immune receptor tyrosine-based inhibitory motif (ITIM)
KeywordsCELL CYCLE / Phosphatase / inhibitory peptide / signal transducer / Src homology-2 domains / immune receptor tyrosine-based inhibitory motif / ITIM
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / negative regulation of immune response / genitalia development / negative regulation of T cell mediated immune response to tumor cell / atrioventricular canal development ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / negative regulation of immune response / genitalia development / negative regulation of T cell mediated immune response to tumor cell / atrioventricular canal development / negative regulation of T cell activation / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / positive regulation of hormone secretion / B cell apoptotic process / positive regulation of T cell apoptotic process / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / hormone metabolic process / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / Regulation of T cell activation by CD28 family / face morphogenesis / Signal regulatory protein family interactions / ERBB signaling pathway / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / negative regulation of B cell apoptotic process / peptide hormone receptor binding / negative regulation of type I interferon production / Interleukin-20 family signaling / Co-inhibition by CTLA4 / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / neurotrophin TRK receptor signaling pathway / inner ear development / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / peptidyl-tyrosine dephosphorylation / humoral immune response / phosphoprotein phosphatase activity / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / ephrin receptor signaling pathway / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / regulation of immune response / Activated NTRK2 signals through FRS2 and FRS3 / regulation of protein-containing complex assembly / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / cell adhesion molecule binding / GPVI-mediated activation cascade / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / hormone-mediated signaling pathway / T cell costimulation / FLT3 Signaling / 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 / cellular response to epidermal growth factor stimulus / positive regulation of mitotic cell cycle / Downstream signal transduction / axonogenesis / positive regulation of interferon-beta production / protein tyrosine kinase binding
Similarity search - Function
Programmed cell death protein 1 / 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 ...Programmed cell death protein 1 / 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 / Immunoglobulin V-Type / SH2 domain / Immunoglobulin V-set domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Immunoglobulin V-set domain / SH2 domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11 / Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKrausze, J. / Sikorska, J. / Carlomagno, T.
CitationJournal: Sci Adv / Year: 2020
Title: Molecular mechanism of SHP2 activation by PD-1 stimulation.
Authors: Marasco, M. / Berteotti, A. / Weyershaeuser, J. / Thorausch, N. / Sikorska, J. / Krausze, J. / Brandt, H.J. / Kirkpatrick, J. / Rios, P. / Schamel, W.W. / Kohn, M. / Carlomagno, T.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 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
D: immune receptor tyrosine-based inhibitory motif (ITIM)
B: Tyrosine-protein phosphatase non-receptor type 11
C: immune receptor tyrosine-based inhibitory motif (ITIM)


Theoretical massNumber of molelcules
Total (without water)26,3794
Polymers26,3794
Non-polymers00
Water46826
1
A: Tyrosine-protein phosphatase non-receptor type 11
D: immune receptor tyrosine-based inhibitory motif (ITIM)


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers13,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area6010 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 11
C: immune receptor tyrosine-based inhibitory motif (ITIM)


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers13,1902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-12 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.856, 29.856, 208.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 3 - 104 / Label seq-ID: 3 - 104

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BC

NCS ensembles : (Details: A, B)

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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 / Shp2 / SH-PTP3


Mass: 11790.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pEMT22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Protein/peptide immune receptor tyrosine-based inhibitory motif (ITIM)


Mass: 1399.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized; Tyr-5 phosphorylated / Source: (synth.) synthetic construct (others) / References: UniProt: Q15116*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.82 Å3/Da / Density % sol: 32.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 31.7% (w/v) PEG3350, 0.1 M HEPES, 0.233 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2016 / Details: Toroidal focusing mirrors
RadiationMonochromator: Double Crystall SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.095→52.06 Å / Num. obs: 10722 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 18.758 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 2.095→2.16 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 2 / Num. unique obs: 889 / CC1/2: 0.526 / Rpim(I) all: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TKZ

3tkz


Resolution: 2.1→52.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / SU B: 20.819 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 513 4.8 %RANDOM
Rwork0.22525 ---
obs0.22794 10137 99.99 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 2.1→52.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 26 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0020.021634
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.972484
X-RAY DIFFRACTIONr_angle_other_deg0.91633790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82924.16796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86215300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7551512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
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_it3.8060.674884
X-RAY DIFFRACTIONr_mcbond_other3.7920.673883
X-RAY DIFFRACTIONr_mcangle_it5.6460.9861098
X-RAY DIFFRACTIONr_mcangle_other5.6450.9881099
X-RAY DIFFRACTIONr_scbond_it6.4241.048952
X-RAY DIFFRACTIONr_scbond_other6.4031.046950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6571.4321386
X-RAY DIFFRACTIONr_long_range_B_refined9.2378.2671977
X-RAY DIFFRACTIONr_long_range_B_other9.2528.2671977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6560 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 30 -
Rwork0.303 778 -
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)
12.8880.6840.27147.28481.32037.39960.1512-0.25770.01220.3951-0.1571-0.19110.2534-0.17590.00590.2704-0.0448-0.01330.0945-0.00250.005913.913-41.31618.892
23.89620.17682.16313.35240.846214.8453-0.0249-0.141-0.1275-0.1521-0.1290.5540.0685-0.47730.1540.559-0.0623-0.02750.1659-0.04920.26356.948-47.78514.176
33.2886-0.7942-0.41377.76481.4747.56690.14010.31150.0104-0.395-0.1737-0.1713-0.2146-0.16360.03360.270.03880.01220.0893-0.00150.0048-1.03-33.339-7.642
46.4467-0.4862-4.12055.7519-0.21111.13570.11280.27740.10740.3167-0.06770.5731-0.3487-0.6331-0.04510.46980.06540.04490.2248-0.0270.2692-8.023-26.715-2.901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 104
2X-RAY DIFFRACTION2D-1 - 7
3X-RAY DIFFRACTION3B3 - 104
4X-RAY DIFFRACTION4C-1 - 7

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