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- PDB-3zm0: Catalytic domain of human SHP2 -

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Basic information

Entry
Database: PDB / ID: 3zm0
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 / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / face morphogenesis / Costimulation by the CD28 family / ERBB signaling pathway / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / triglyceride metabolic process / organ growth / negative regulation of type I interferon production / peptide hormone receptor binding / CTLA4 inhibitory signaling / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / PI-3K cascade:FGFR2 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / Prolactin receptor signaling / MAPK3 (ERK1) activation / regulation of cell adhesion mediated by integrin / PECAM1 interactions / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / 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 / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / 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 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / GPVI-mediated activation cascade / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / cell adhesion molecule binding / T cell costimulation / cellular response to epidermal growth factor stimulus / FLT3 Signaling / protein dephosphorylation / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / Downstream signal transduction / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / 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 FGFR3 signaling / Negative regulation of FGFR2 signaling / insulin receptor binding / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT
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)33,1101
Polymers33,1101
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.216, 42.257, 49.197
Angle α, β, γ (deg.)72.52, 81.63, 74.73
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: 33109.609 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.: 206 / 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: 2.32 Å3/Da / Density % sol: 46.92 % / 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: 40770 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.4
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 5.5 / % possible all: 51.6

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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→19.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.178 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 256-262, 314-323 AND 407-410 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21342 2107 5 %RANDOM
Rwork0.18413 ---
obs0.18559 40031 85.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0.19 Å20.01 Å2
2--0.34 Å20.33 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 0 206 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9342984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88523.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11215399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5911517
X-RAY DIFFRACTIONr_chiral_restr0.130.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021678
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21007
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21508
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.52421342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34432129
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7235993
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.377852
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
Rfree0.242 88 -
Rwork0.201 1675 -
obs--100 %
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)
15.7605-3.74-5.69974.95423.52478.78880.1787-0.1381-0.0516-0.1481-0.0082-0.1019-0.11970.1104-0.17050.1091-0.0246-0.01640.01840.02730.004820.788524.096148.8671
22.20110.1652-0.33952.303-0.52183.91910.11060.0639-0.0999-0.0829-0.0805-0.19970.71130.4018-0.03010.14050.0758-0.0334-0.0049-0.02150.011526.632418.033820.7183
30.15120.1035-0.86830.1-0.21599.90910.004-0.002-0.0120.0644-0.0042-0.0210.26140.26990.00020.1099-0.0049-0.02990.044-0.01470.025218.775922.93878.0009
41.3246-0.3748-0.71771.93110.59685.72380.10860.1189-0.0589-0.0124-0.05810.08910.3074-0.1978-0.05050.0995-0.0095-0.0250.0058-0.0050.041519.132522.812318.5619
55.61410.002-2.50652.085-0.48285.83810.0143-0.039-0.0406-0.01040.01110.11270.16-0.0734-0.02540.10350.0003-0.01720.0438-0.00570.079619.661529.662322.4517
61.6921-0.2299-0.73761.30660.83322.5418-0.02360.1098-0.0462-0.1069-0.01970.06020.1009-0.07040.04340.0622-0.0025-0.00790.03830.00360.038816.452233.35514.953
711.5164-0.3607-1.54860.77280.45941.8803-0.0209-0.3412-0.02840.04530.0265-0.1508-0.03750.3692-0.00560.016-0.0225-0.01160.07630.0090.054132.32237.764926.33
81.1368-1.91071.45714.3631-2.94042.2909-0.00360.11250.13550.0046-0.0132-0.1101-0.31320.26670.01680.062-0.05470.01010.05190.02730.024925.076245.15114.7872
90.5637-1.3646-0.15066.24422.40822.83140.07280.11490.0556-0.424-0.1437-0.0966-0.24240.00540.07090.1051-0.02540.01380.01890.02770.010419.846843.22979.1189
102.03161.20071.80943.846-0.21955.8021-0.06340.00020.14670.3705-0.0895-0.0208-0.54370.07870.15290.1152-0.0282-0.0109-0.02730.00830.030120.346248.740825.2778
112.518-1.06550.74122.2094-0.13346.39060.04110.3105-0.0558-0.4632-0.08650.1282-0.1279-0.35120.04540.0781-0.0024-0.02060.0550.00620.048413.093841.240212.6317
122.828-0.3992.91070.4972-1.67326.6105-0.04140.08650.13450.1035-0.1133-0.1126-0.2040.53640.15460.0637-0.0381-0.01320.0277-0.00860.036827.229641.330834.5037
134.8162-0.26174.65540.63360.63155.7838-0.116-0.23110.16720.0762-0.04440.0786-0.2209-0.41620.16030.0520.00120.00130.03760.00050.032912.423442.346532.7587
140.9081-0.11540.47580.7879-0.23761.95350.0083-0.05840.00420.08730.01170.07790.0006-0.1789-0.020.0514-0.01710.00240.0328-0.00120.047815.360433.205731.232
150.1206-0.44581.71146.57096.1655.97680.176-0.4354-0.3929-0.60280.6640.05712.3662-0.9001-0.840.1580.0228-0.03220.18520.13650.17334.565330.919445.871
160.3322-0.09420.51681.57130.74564.51030.0353-0.0549-0.01140.140.06790.06130.352-0.2377-0.10320.1063-0.0336-0.02250.01080.01150.027218.002722.123136.1322
173.8167-1.5674-0.02374.24111.02223.583-0.0189-0.17960.00760.22270.077-0.0310.10270.0241-0.05810.095-0.0222-0.00470.04840.00740.034922.390932.318943.7345
1817.2668-8.38111.705511.0456-7.439.7138-0.3622-0.87471.07680.82890.30340.0552-0.6793-0.6990.05880.05350.11260.04960.0661-0.04760.01310.192141.08146.1748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 254
2X-RAY DIFFRACTION2A255 - 288
3X-RAY DIFFRACTION3A289 - 299
4X-RAY DIFFRACTION4A300 - 312
5X-RAY DIFFRACTION5A313 - 337
6X-RAY DIFFRACTION6A338 - 353
7X-RAY DIFFRACTION7A354 - 366
8X-RAY DIFFRACTION8A367 - 377
9X-RAY DIFFRACTION9A378 - 389
10X-RAY DIFFRACTION10A390 - 401
11X-RAY DIFFRACTION11A402 - 417
12X-RAY DIFFRACTION12A418 - 431
13X-RAY DIFFRACTION13A432 - 448
14X-RAY DIFFRACTION14A449 - 480
15X-RAY DIFFRACTION15A481 - 488
16X-RAY DIFFRACTION16A489 - 505
17X-RAY DIFFRACTION17A506 - 520
18X-RAY DIFFRACTION18A521 - 525

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