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- PDB-3zm3: Catalytic domain of human SHP2 -

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Basic information

Entry
Database: PDB / ID: 3zm3
TitleCatalytic domain of human SHP2
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11
KeywordsHYDROLASE / PTP1B
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 / multicellular organismal reproductive process / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / multicellular organismal reproductive process / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation / positive regulation of hormone secretion / Interleukin-37 signaling / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / face morphogenesis / Costimulation by the CD28 family / triglyceride metabolic process / ERBB signaling pathway / Signal regulatory protein family interactions / organ growth / platelet formation / megakaryocyte development / negative regulation of type I interferon production / peptide hormone receptor binding / Platelet sensitization by LDL / CTLA4 inhibitory signaling / PI-3K cascade:FGFR2 / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR4 / Prolactin receptor signaling / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / PECAM1 interactions / regulation of cell adhesion mediated by integrin / MAPK1 (ERK2) activation / regulation of type I interferon-mediated signaling pathway / Bergmann glial cell differentiation / neurotrophin TRK receptor signaling pathway / inner ear development / phosphoprotein phosphatase activity / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / PI3K Cascade / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / fibroblast growth factor receptor signaling pathway / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / PD-1 signaling / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / positive regulation of insulin receptor signaling pathway / cell adhesion molecule binding / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR4 signaling / homeostasis of number of cells within a tissue / GPVI-mediated activation cascade / Tie2 Signaling / FRS-mediated FGFR1 signaling / FLT3 Signaling / T cell costimulation / cellular response to epidermal growth factor stimulus / phosphotyrosine residue binding / protein dephosphorylation / positive regulation of interferon-beta production / hormone-mediated signaling pathway / protein tyrosine kinase binding / Downstream signal transduction / positive regulation of mitotic cell cycle / axonogenesis / protein-tyrosine-phosphatase / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein tyrosine phosphatase activity / DNA damage checkpoint signaling / integrin-mediated signaling pathway / positive regulation of D-glucose import / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / insulin receptor binding / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / brain development / epidermal growth factor receptor signaling pathway
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / 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: 1.5 Å
AuthorsBohm, K. / Schuetz, A. / Roske, Y. / Heinemann, U.
CitationJournal: Chemmedchem / Year: 2015
Title: Selective Inhibitors of the Protein Tyrosine Phosphatase Shp2 Block Cellular Motility and Growth of Cancer Cells in Vitro and in Vivo.
Authors: Grosskopf, S. / Eckert, C. / Arkona, C. / Radetzki, S. / Bohm, K. / Heinemann, U. / Wolber, G. / Von Kries, J. / Birchmeier, W. / Rademann, J.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)33,1641
Polymers33,1641
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.190, 42.091, 49.386
Angle α, β, γ (deg.)71.99, 81.09, 75.36
Int Tables number1
Space group name H-MP1

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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: 33163.660 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 248-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7HT (MODIFIED PET) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): SCS1 ROSETTA T1R / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.31 Å3/Da / Density % sol: 46.84 % / Description: NONE
Crystal growDetails: 16-22% (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 39749 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 3.4 / % possible all: 50.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7O
Resolution: 1.5→19.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.755 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 255-262 AND 314-321 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22747 2126 5.1 %RANDOM
Rwork0.19056 ---
obs0.19249 39569 87.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.745 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0.14 Å2-0.22 Å2
2---0.52 Å20.45 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 0 221 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9353081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98723.782119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24815413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0271519
X-RAY DIFFRACTIONr_chiral_restr0.1520.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.21099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.54921383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12632196
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.654.51026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0586879
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 94 -
Rwork0.233 1699 -
obs--51.24 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.0807-2.7416-4.36564.3711.8958.167-0.0441-0.0424-0.0731-0.1295-0.0272-0.14020.03220.1680.07130.0632-0.01250.0020.0130.03140.028922.079824.904948.9359
22.87880.5279-0.51882.06540.19563.35650.1262-0.0625-0.15960.0042-0.0737-0.20640.53430.2935-0.05250.10120.0569-0.0271-0.0003-0.01130.018327.535318.512520.9283
30.30330.1178-0.3370.0514-0.33197.49850.00060.0174-0.0050.0405-0.0323-0.03990.34780.22050.03170.08820.0104-0.01570.0196-0.01410.010320.380322.55877.9809
43.0329-1.944-1.22571.94550.46173.3715-0.0381-0.0639-0.2230.18070.07260.38040.1831-0.4939-0.03450.0434-0.02880.01590.04450.00780.056113.633726.364625.8946
56.60160.4508-3.17820.83280.4074.8907-0.00530.0191-0.1097-0.01790.02530.03620.0936-0.0106-0.020.02180.00750.00730.00660.01320.031119.587829.937924.5635
67.0883-0.9315.94227.3724.51328.8470.07140.3163-0.0659-0.41240.0748-0.4457-0.08910.6422-0.14610.030.02030.04880.05560.01260.046330.332.017113.8399
71.57830.0801-0.36791.70570.96361.8028-0.02380.0713-0.0625-0.1025-0.02570.06230.147-0.05680.04950.039-0.0034-0.00390.02170.00520.023716.641233.691215.0871
89.3813-1.159-1.23210.34050.42931.3685-0.0622-0.3327-0.0632-0.04410.0276-0.1806-0.00450.27490.0347-0.0075-0.00160.00340.05350.01850.054133.000938.714426.4561
91.6981-1.89260.55345.2163-1.58991.77950.02850.02350.0958-0.0604-0.0808-0.2021-0.1570.21530.05230.0159-0.0290.01160.0660.01090.039827.657342.619717.2808
101.9005-2.3498-1.324324.686710.542912.27340.13670.0781-0.0998-0.138-0.3148-0.3682-0.08480.06750.17810.0153-0.01810.03690.03890.03310.039822.743347.60078.5652
110.5624-0.12050.12953.24490.32122.838-0.00810.02030.0261-0.0347-0.0212-0.0345-0.2875-0.00210.02920.0413-0.01660.00740.03260.01230.061920.476646.641518.0167
124.9532-0.3446-0.65327.9554-0.49157.19560.10490.6077-0.1081-0.8423-0.27170.41790.4363-0.51140.16680.06920.0006-0.02190.0687-0.0076-0.006114.427340.16347.4443
131.9164-0.24731.00882.93-0.36934.09-0.06540.22580.0446-0.06890.01010.0519-0.180.06670.05540.0080.00770.02110.02810.00880.045718.497842.94221.6466
147.6458-0.6841-0.46186.8026-0.135412.7946-0.0763-0.0470.24750.0753-0.043-0.4350.12250.50430.11920.0435-0.0145-0.02550.0629-0.00150.072731.214739.908739.5885
154.9588-0.3594.16061.6232-0.02245.825-0.1233-0.18260.13380.03110.05340.0801-0.1632-0.33590.06990.03140.01510.00660.02170.01250.015715.149443.151534.737
160.8713-0.37780.21720.7139-0.21751.459-0.00390.00090.00320.01820.03860.0892-0.0021-0.1116-0.03470.0175-0.01180.00370.02180.00690.035915.759734.452929.8977
175.56054.0664-3.49539.9287-5.81910.8024-0.0509-0.2936-0.05570.15870.10530.16970.3427-0.3773-0.0544-0.02680.05670.06080.12640.04390.03715.213633.700243.6713
181.6298-0.1893-0.66131.33280.43546.6778-0.0353-0.1883-0.01180.07770.06730.17530.1901-0.3742-0.0320.0467-0.0075-0.00590.01010.01670.028317.085222.864737.7215
199.52923.91572.71166.99923.59996.4581-0.07840.2201-0.18160.10880.2065-0.17960.21270.3776-0.12810.04740.00550.00050.00540.01090.011827.657427.873938.3167
204.8354-1.4795-0.24183.8547-0.61972.4676-0.0893-0.26480.24660.29590.12150.1714-0.1692-0.2774-0.03220.05120.01970.01210.046-0.00580.005117.601237.042745.6963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 254
2X-RAY DIFFRACTION2A255 - 288
3X-RAY DIFFRACTION3A289 - 303
4X-RAY DIFFRACTION4A304 - 325
5X-RAY DIFFRACTION5A326 - 332
6X-RAY DIFFRACTION6A333 - 338
7X-RAY DIFFRACTION7A339 - 353
8X-RAY DIFFRACTION8A354 - 365
9X-RAY DIFFRACTION9A366 - 374
10X-RAY DIFFRACTION10A375 - 379
11X-RAY DIFFRACTION11A380 - 400
12X-RAY DIFFRACTION12A401 - 408
13X-RAY DIFFRACTION13A409 - 423
14X-RAY DIFFRACTION14A424 - 431
15X-RAY DIFFRACTION15A432 - 444
16X-RAY DIFFRACTION16A445 - 478
17X-RAY DIFFRACTION17A479 - 486
18X-RAY DIFFRACTION18A487 - 502
19X-RAY DIFFRACTION19A503 - 510
20X-RAY DIFFRACTION20A511 - 525

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