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- PDB-2nz6: Crystal structure of the PTPRJ inactivating mutant C1239S -

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Basic information

Entry
Database: PDB / ID: 2nz6
TitleCrystal structure of the PTPRJ inactivating mutant C1239S
ComponentsReceptor-type tyrosine-protein phosphatase eta
KeywordsHYDROLASE / HYDROLASE RECEPTOR TYPE TYROSINE PHOSPHATASE J / PTPRJ / GLYCOPROTEIN / PROTEIN PHOSPHATASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / mitogen-activated protein kinase binding / negative regulation of platelet-derived growth factor receptor signaling pathway / platelet formation ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / mitogen-activated protein kinase binding / negative regulation of platelet-derived growth factor receptor signaling pathway / platelet formation / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of macrophage chemotaxis / Phosphorylation of CD3 and TCR zeta chains / negative regulation of epidermal growth factor receptor signaling pathway / oligodendrocyte differentiation / phosphatase activity / peptidyl-tyrosine dephosphorylation / platelet-derived growth factor receptor signaling pathway / immunological synapse / positive regulation of focal adhesion assembly / negative regulation of MAP kinase activity / regulation of cell adhesion / vasculogenesis / specific granule membrane / positive regulation of phagocytosis / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / Negative regulation of FLT3 / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / B cell differentiation / positive regulation of calcium-mediated signaling / axon guidance / negative regulation of cell migration / negative regulation of cell growth / cytokine-mediated signaling pathway / Negative regulation of MET activity / beta-catenin binding / ruffle membrane / positive regulation of tumor necrosis factor production / blood coagulation / cell junction / glucose homeostasis / cell-cell junction / T cell receptor signaling pathway / heart development / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / nuclear body / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Receptor-type tyrosine-protein phosphatase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUgochukwu, E. / Barr, A. / Savitsky, P. / Pike, A.C.W. / Bunkoczi, G. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. ...Ugochukwu, E. / Barr, A. / Savitsky, P. / Pike, A.C.W. / Bunkoczi, G. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / 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
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2908
Polymers36,8671
Non-polymers4247
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Receptor-type tyrosine-protein phosphatase eta
hetero molecules

A: Receptor-type tyrosine-protein phosphatase eta
hetero molecules

A: Receptor-type tyrosine-protein phosphatase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,87124
Polymers110,6003
Non-polymers1,27221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10470 Å2
ΔGint-168 kcal/mol
Surface area36090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.521, 88.521, 118.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-206-

NI

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase eta / Protein-tyrosine phosphatase eta / R-PTP-eta / HPTP eta / Protein- tyrosine phosphatase receptor ...Protein-tyrosine phosphatase eta / R-PTP-eta / HPTP eta / Protein- tyrosine phosphatase receptor type J / Density-enhanced phosphatase 1 / DEP-1 / CD148 antigen


Mass: 36866.551 Da / Num. of mol.: 1 / Fragment: Tyrosine-protein phosphatase / Mutation: C1239S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRJ / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q12913, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01M NiCl2, 0.1M TRIS, pH 8.5, 1M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→46.98 Å / Num. obs: 15274 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.387 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2CFV

2cfv


Resolution: 2.3→46.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.948 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 738 4.8 %RANDOM
Rwork0.18179 ---
all0.18399 14581 --
obs0.18399 14581 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 11 94 2485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212458
X-RAY DIFFRACTIONr_bond_other_d0.0010.021594
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9293345
X-RAY DIFFRACTIONr_angle_other_deg1.31433880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25724.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined0.1990.2444
X-RAY DIFFRACTIONr_nbd_other0.1980.21603
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21202
X-RAY DIFFRACTIONr_nbtor_other0.0870.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2106
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.25
X-RAY DIFFRACTIONr_mcbond_it0.5961.51533
X-RAY DIFFRACTIONr_mcbond_other0.1071.5592
X-RAY DIFFRACTIONr_mcangle_it0.97822398
X-RAY DIFFRACTIONr_scbond_it1.39131087
X-RAY DIFFRACTIONr_scangle_it1.9014.5947
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 57 -
Rwork0.227 968 -
obs--89.6 %
Refinement TLS params.Method: refined / Origin x: -7.3409 Å / Origin y: 29.388 Å / Origin z: -13.9498 Å
111213212223313233
T-0.0848 Å2-0.0195 Å20.0105 Å2--0.126 Å20.0067 Å2---0.1298 Å2
L0.9952 °2-0.2978 °2-0.1515 °2-1.915 °2-0.6791 °2--1.4601 °2
S-0.0626 Å °-0.1023 Å °-0.1365 Å °0.1607 Å °0.0587 Å °0.0983 Å °0.1221 Å °-0.0931 Å °0.0039 Å °

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