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- PDB-3b7o: Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11)... -

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Basic information

Entry
Database: PDB / ID: 3b7o
TitleCrystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible active site
ComponentsTyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE / SHP2 / PTPN11 / tyrosine phosphatase / Structural Genomics / Structural Genomics Consortium / SGC / Deafness / Disease mutation / Phosphorylation / Protein phosphatase / SH2 domain
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 / Netrin mediated repulsion signals / positive regulation of hormone secretion ...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 / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / ERBB signaling pathway / face morphogenesis / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / CTLA4 inhibitory signaling / triglyceride metabolic process / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / PECAM1 interactions / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / 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 / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / 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 / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / Downstream signal transduction / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / insulin receptor binding / epidermal growth factor receptor signaling pathway / multicellular organism growth
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
D-MALATE / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUgochukwu, E. / Barr, A. / Patel, A. / King, O. / Niesen, F. / Salah, E. / Savitsky, P. / Pilka, E.S. / Elkins, J. / Arrowsmith, C.H. ...Ugochukwu, E. / Barr, A. / Patel, A. / King, O. / Niesen, F. / Salah, E. / Savitsky, P. / Pilka, E.S. / Elkins, J. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0142
Polymers36,8801
Non-polymers1341
Water4,342241
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.813, 86.496, 166.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11 / Protein-tyrosine phosphatase 2C / PTP-2C / PTP-1D / SH-PTP3 / SH-PTP2 / SHP-2 / Shp2


Mass: 36879.723 Da / Num. of mol.: 1 / Fragment: 'Residues 237-529 (Isoform 2)'
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.15 M Na Malate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00721 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00721 Å / Relative weight: 1
ReflectionResolution: 1.6→34.12 Å / Num. all: 43184 / Num. obs: 43184 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 13.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2 / Num. unique all: 25196 / Rsym value: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2SHP

2shp


Resolution: 1.6→34.12 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.422 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20897 2157 5.1 %RANDOM
Rwork0.17009 ---
all0.17204 40383 --
obs0.17204 40383 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 9 241 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222274
X-RAY DIFFRACTIONr_bond_other_d0.0020.021559
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9433082
X-RAY DIFFRACTIONr_angle_other_deg0.9633793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3855282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54823.894113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8651518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.2150.2422
X-RAY DIFFRACTIONr_nbd_other0.2020.21656
X-RAY DIFFRACTIONr_nbtor_refined0.180.21141
X-RAY DIFFRACTIONr_nbtor_other0.0870.21143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.218
X-RAY DIFFRACTIONr_mcbond_it1.4071.51489
X-RAY DIFFRACTIONr_mcbond_other0.3491.5556
X-RAY DIFFRACTIONr_mcangle_it1.89622230
X-RAY DIFFRACTIONr_scbond_it3.0253995
X-RAY DIFFRACTIONr_scangle_it4.4554.5846
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 134 -
Rwork0.247 2524 -
obs--85.14 %
Refinement TLS params.Method: refined / Origin x: 17.0831 Å / Origin y: 10.0483 Å / Origin z: 63.979 Å
111213212223313233
T-0.045 Å2-0.0118 Å20.0223 Å2--0.0346 Å2-0.0009 Å2---0.0369 Å2
L0.5539 °2-0.2514 °2-0.2284 °2-1.0365 °20.2766 °2--0.75 °2
S0.0242 Å °-0.0188 Å °0.0185 Å °-0.0773 Å °0.0019 Å °-0.0581 Å °0.0009 Å °-0.0354 Å °-0.0261 Å °

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