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- PDB-8yhi: The Crystal Structure of SHP1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8yhi
TitleThe Crystal Structure of SHP1 from Biortus.
ComponentsTyrosine-protein phosphatase non-receptor type 6
KeywordsHYDROLASE / Protein phosphatase
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / negative regulation of T cell receptor signaling pathway / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / negative regulation of MAPK cascade / regulation of G1/S transition of mitotic cell cycle / PECAM1 interactions / negative regulation of interleukin-6 production / regulation of type I interferon-mediated signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / T cell proliferation / Regulation of IFNG signaling / Growth hormone receptor signaling / negative regulation of T cell proliferation / GPVI-mediated activation cascade / T cell costimulation / cell adhesion molecule binding / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / SH3 domain binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / specific granule lumen / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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
Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of SHP1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2345
Polymers32,9181
Non-polymers3164
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-38 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.302, 56.498, 110.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-880-

HOH

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / ...Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / Protein-tyrosine phosphatase SHP-1 / SH-PTP1


Mass: 32918.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN6, HCP, PTP1C / Production host: Escherichia coli (E. coli) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7.5, 2% PEG 400, 2.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.75→45.3 Å / Num. obs: 29341 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.975 / Num. unique obs: 1593

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.488 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.192 / SU B: 2.468 / SU ML: 0.08 / Average fsc free: 0.9632 / Average fsc work: 0.9737 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2266 1420 4.851 %
Rwork0.1925 27850 -
all0.194 --
obs-29270 99.836 %
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: 30.129 Å2
Baniso -1Baniso -2Baniso -3
1--1.927 Å2-0 Å20 Å2
2--1.386 Å2-0 Å2
3---0.541 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 18 185 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162181
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.8223160
X-RAY DIFFRACTIONr_angle_other_deg0.4041.7765023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.274515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29410410
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.51810119
X-RAY DIFFRACTIONr_chiral_restr0.0580.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_nbd_refined0.20.2448
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21968
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.219
X-RAY DIFFRACTIONr_nbd_other0.1780.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.227
X-RAY DIFFRACTIONr_mcbond_it1.5873.0411122
X-RAY DIFFRACTIONr_mcbond_other1.5863.0411122
X-RAY DIFFRACTIONr_mcangle_it2.5835.4511400
X-RAY DIFFRACTIONr_mcangle_other2.5825.4531401
X-RAY DIFFRACTIONr_scbond_it2.1373.3641211
X-RAY DIFFRACTIONr_scbond_other2.1373.3651212
X-RAY DIFFRACTIONr_scangle_it3.5396.0521758
X-RAY DIFFRACTIONr_scangle_other3.5386.0521759
X-RAY DIFFRACTIONr_lrange_it5.23432.9792674
X-RAY DIFFRACTIONr_lrange_other5.18332.4642652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.2661130.24519890.24621050.9450.95799.85750.245
1.795-1.8440.281950.22919920.23120880.9460.96399.95210.229
1.844-1.8980.2461080.20919120.21120200.9560.9691000.209
1.898-1.9560.296860.20618820.2119680.9450.971000.206
1.956-2.020.218970.19817990.19918970.9710.97599.94730.198
2.02-2.0910.237840.17317740.17518580.9660.9811000.173
2.091-2.1690.192730.18117150.18117880.9750.9791000.181
2.169-2.2580.221850.17816370.1817230.9710.97999.9420.178
2.258-2.3580.205830.17615610.17816440.9760.981000.176
2.358-2.4720.199710.17915040.1815750.9730.981000.179
2.472-2.6060.186780.18614280.18615080.9780.97999.86740.186
2.606-2.7630.245700.19313590.19614290.9560.9761000.193
2.763-2.9530.251660.19712930.213600.9650.97699.92650.197
2.953-3.1880.249620.18712060.1912680.9650.9771000.187
3.188-3.490.213590.19211170.19311800.9740.97699.6610.192
3.49-3.8980.226490.18510010.18710520.9710.97799.80990.185
3.898-4.4940.196420.1779190.1789650.9710.97899.58550.177
4.494-5.4860.204450.1977610.1988210.9680.97298.1730.197
5.486-7.6840.311390.2386160.2426570.940.96599.69560.238
7.684-39.4880.208150.1993850.1994080.980.97198.03920.199

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