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

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Basic information

Entry
Database: PDB / ID: 6roz
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 switch motif
Components
  • Tyrosine-protein phosphatase non-receptor type 11
  • immune receptor tyrosine-based switch motif (ITSM)
KeywordsCELL CYCLE / Phosphatase / inhibitory peptide / signal transducer / Src homology-2 domains / ITSM / immune receptor tyrosine-based switch motif
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 / atrioventricular canal development / negative regulation of T cell mediated immune response to tumor cell ...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 / atrioventricular canal development / negative regulation of T cell mediated immune response to tumor cell / negative regulation of cell adhesion mediated by integrin / negative regulation of T cell activation / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / cerebellar cortex formation / positive regulation of T cell apoptotic process / positive regulation of hormone secretion / B cell apoptotic process / regulation of protein export from nucleus / Interleukin-37 signaling / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of ossification / Signaling by Leptin / MET activates PTPN11 / hormone metabolic process / 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 / negative regulation of B cell apoptotic process / organ growth / megakaryocyte development / Interleukin-20 family signaling / negative regulation of type I interferon production / Interleukin-6 signaling / PI-3K cascade:FGFR3 / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / humoral immune response / phosphoprotein phosphatase activity / positive regulation of intracellular signal transduction / Regulation of IFNA/IFNB signaling / RET 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 / regulation of immune response / regulation of protein-containing complex assembly / Regulation of IFNG signaling / Activated NTRK2 signals through FRS2 and FRS3 / GPVI-mediated activation cascade / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / cell adhesion molecule binding / negative regulation of T cell proliferation / T cell costimulation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / hormone-mediated signaling pathway / FRS-mediated FGFR1 signaling / Tie2 Signaling / phosphotyrosine residue binding / protein-tyrosine-phosphatase / FLT3 Signaling / Downstream signal transduction / homeostasis of number of cells within a tissue / positive regulation of mitotic cell cycle / axonogenesis / 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
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / SH2 domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin V-set domain / 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: 2.89 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 23, 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: immune receptor tyrosine-based switch motif (ITSM)
C: Tyrosine-protein phosphatase non-receptor type 11
D: immune receptor tyrosine-based switch motif (ITSM)


Theoretical massNumber of molelcules
Total (without water)26,3354
Polymers26,3354
Non-polymers00
Water00
1
A: Tyrosine-protein phosphatase non-receptor type 11
B: immune receptor tyrosine-based switch motif (ITSM)


Theoretical massNumber of molelcules
Total (without water)13,1682
Polymers13,1682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-12 kcal/mol
Surface area6170 Å2
MethodPISA
2
C: Tyrosine-protein phosphatase non-receptor type 11
D: immune receptor tyrosine-based switch motif (ITSM)


Theoretical massNumber of molelcules
Total (without water)13,1682
Polymers13,1682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-14 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.035, 30.035, 213.113
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
21C

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
2CC

NCS ensembles : (Details: A, C)

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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 switch motif (ITSM)


Mass: 1377.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized peptide / Source: (synth.) synthetic construct (others) / References: UniProt: Q15116*PLUS
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: 1.85 Å3/Da / Density % sol: 34.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 31.7% (w/v) PEG 3350, 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 CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.89→53.28 Å / Num. obs: 4283 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 61.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.074 / Net I/σ(I): 10.4
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 2 / Num. unique obs: 713 / CC1/2: 0.764 / Rpim(I) all: 0.552 / % 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: 2.89→53.28 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.914 / SU B: 67.134 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28462 418 9.9 %RANDOM
Rwork0.23943 ---
obs0.24372 3811 99.98 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 70.991 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.89→53.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 0 0 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191850
X-RAY DIFFRACTIONr_bond_other_d0.0040.021660
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9692508
X-RAY DIFFRACTIONr_angle_other_deg0.97833850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87323.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2981512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
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_it0.1253.708892
X-RAY DIFFRACTIONr_mcbond_other0.1263.709891
X-RAY DIFFRACTIONr_mcangle_it0.2365.5611108
X-RAY DIFFRACTIONr_mcangle_other0.2365.5611109
X-RAY DIFFRACTIONr_scbond_it0.0633.727958
X-RAY DIFFRACTIONr_scbond_other0.0633.727959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.135.5911401
X-RAY DIFFRACTIONr_long_range_B_refined1.04169.8397083
X-RAY DIFFRACTIONr_long_range_B_other1.04169.8347082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6222 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 23 -
Rwork0.381 308 -
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)
110.9460.1989-1.43034.5686-0.87878.5362-0.4982-0.77720.32250.28280.25310.07330.01980.14310.24510.16290.1605-0.01290.3384-0.02590.021941.19-16.1321.182
210.67925.3609-8.17149.2143-8.917129.6902-0.5070.1964-0.2132-0.12890.6382-0.39880.9155-1.2439-0.13120.18220.1749-0.08380.4059-0.02140.231348.313-23.93417.562
310.6425-0.2924-1.16143.65811.05617.5465-0.36870.79340.149-0.27060.16730.2174-0.0605-0.1360.20140.1673-0.15-0.0310.34910.03460.019733.951-1.083-6.345
44.5435-4.111-1.759212.195811.597633.8459-0.5302-0.2243-0.1544-0.08710.35390.70690.74970.82870.17620.2839-0.1836-0.02530.5081-0.00780.184926.865-9.229-2.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 104
2X-RAY DIFFRACTION2B2 - 11
3X-RAY DIFFRACTION3C3 - 104
4X-RAY DIFFRACTION4D2 - 11

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