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- PDB-8wfy: The Crystal Structure of SHP2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wfy
TitleThe Crystal Structure of SHP2 from Biortus.
ComponentsTyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE / Protein phosphatase
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 / negative regulation of chondrocyte differentiation / Signaling by Leptin / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / triglyceride metabolic process / platelet formation / negative regulation of type I interferon production / megakaryocyte development / organ growth / CTLA4 inhibitory signaling / 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 / phosphoprotein phosphatase activity / inner ear development / MAPK1 (ERK2) activation / PECAM1 interactions / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / regulation of type I interferon-mediated 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 / PI3K Cascade / Regulation of IFNA/IFNB signaling / PD-1 signaling / negative regulation of insulin secretion / 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 / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / homeostasis of number of cells within a tissue / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / cellular response to epidermal growth factor stimulus / FRS-mediated FGFR1 signaling / GPVI-mediated activation cascade / Tie2 Signaling / protein tyrosine kinase binding / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / cell adhesion molecule binding / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / axonogenesis / Downstream signal transduction / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / positive regulation of glucose import / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / brain development / Spry regulation of FGF signaling / multicellular organism growth / insulin receptor binding
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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 ...Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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
Similarity search - Domain/homology
Chem-5OD / Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of SHP2 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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: Tyrosine-protein phosphatase non-receptor type 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0684
Polymers120,3642
Non-polymers7052
Water7,638424
1
A: Tyrosine-protein phosphatase non-receptor type 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5342
Polymers60,1821
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5342
Polymers60,1821
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.617, 213.636, 55.707
Angle α, β, γ (deg.)90.000, 96.846, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 525 / Label seq-ID: 4 - 525

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11


Mass: 60181.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124
#2: Chemical ChemComp-5OD / 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine / SHP099


Mass: 352.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19Cl2N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1% Tryptone, 0.001M NaN3, 0.05M HEPEs-Na pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.12 Å / Num. obs: 32048 / % possible obs: 98.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.2
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.319 / Num. unique obs: 3907

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.12 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.826 / SU B: 18.468 / SU ML: 0.401 / Cross valid method: FREE R-VALUE / ESU R Free: 0.442
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3171 1564 4.886 %
Rwork0.2367 30445 -
all0.241 --
obs-32009 98.735 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.279 Å2
Baniso -1Baniso -2Baniso -3
1-4.017 Å20 Å20.065 Å2
2---2.343 Å20 Å2
3----1.643 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 46 424 8390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177681
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.64810995
X-RAY DIFFRACTIONr_angle_other_deg1.171.58617680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37822.09469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.043151462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8941562
X-RAY DIFFRACTIONr_chiral_restr0.0560.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021915
X-RAY DIFFRACTIONr_nbd_refined0.1750.21520
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.27486
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23741
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.24203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2353
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.243
X-RAY DIFFRACTIONr_nbd_other0.1890.2144
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3710.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1430.21
X-RAY DIFFRACTIONr_mcbond_it2.1223.623914
X-RAY DIFFRACTIONr_mcbond_other2.1223.623913
X-RAY DIFFRACTIONr_mcangle_it3.5555.4174873
X-RAY DIFFRACTIONr_mcangle_other3.5555.4174874
X-RAY DIFFRACTIONr_scbond_it1.8233.7584228
X-RAY DIFFRACTIONr_scbond_other1.8233.7574229
X-RAY DIFFRACTIONr_scangle_it3.085.5556119
X-RAY DIFFRACTIONr_scangle_other3.085.5546120
X-RAY DIFFRACTIONr_lrange_it7.51366.08933983
X-RAY DIFFRACTIONr_lrange_other7.49566.17533809
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0515469
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.100380.05009
12AX-RAY DIFFRACTIONLocal ncs0.100380.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.3741310.262261X-RAY DIFFRACTION98.1535
2.668-2.7410.3271020.2652141X-RAY DIFFRACTION98.291
2.741-2.820.3391130.2512161X-RAY DIFFRACTION98.8696
2.82-2.9070.356950.2392058X-RAY DIFFRACTION98.7162
2.907-3.0020.3231060.2451967X-RAY DIFFRACTION98.8555
3.002-3.1070.2921150.241957X-RAY DIFFRACTION98.6197
3.107-3.2240.346820.2441890X-RAY DIFFRACTION98.4032
3.224-3.3560.317820.2461774X-RAY DIFFRACTION98.253
3.356-3.5050.3711100.2491756X-RAY DIFFRACTION98.6779
3.505-3.6760.313850.2271618X-RAY DIFFRACTION99.1269
3.676-3.8750.298860.221578X-RAY DIFFRACTION98.9887
3.875-4.1090.296730.2191484X-RAY DIFFRACTION99.1088
4.109-4.3920.25760.1991399X-RAY DIFFRACTION99.193
4.392-4.7440.313660.211326X-RAY DIFFRACTION99.0043
4.744-5.1950.303740.2111186X-RAY DIFFRACTION98.9788
5.195-5.8070.334510.2611098X-RAY DIFFRACTION99.2228
5.807-6.7020.328420.262970X-RAY DIFFRACTION98.7317
6.702-8.20.29330.264815X-RAY DIFFRACTION99.0654
8.2-11.5630.329290.228652X-RAY DIFFRACTION98.8389
11.563-49.120.276130.276354X-RAY DIFFRACTION98.3914

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