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- PDB-2cfv: Crystal structure of human protein tyrosine phosphatase receptor ... -

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Basic information

Entry
Database: PDB / ID: 2cfv
TitleCrystal structure of human protein tyrosine phosphatase receptor type J
ComponentsHUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
KeywordsHYDROLASE / RECEPTOR TYPE TYROSINE PHOSPHATASE J / PTPRJ / GLYCOPROTEIN / PROTEIN PHOSPHATASE
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway / positive regulation of macrophage chemotaxis / positive chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / phosphatase activity / positive regulation of focal adhesion assembly / platelet-derived growth factor receptor signaling pathway / : / immunological synapse / positive regulation of cell adhesion / peptidyl-tyrosine dephosphorylation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of cell adhesion / specific granule membrane / positive regulation of phagocytosis / Negative regulation of FLT3 / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / protein-tyrosine-phosphatase / B cell differentiation / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / Negative regulation of MET activity / negative regulation of cell growth / beta-catenin binding / cytokine-mediated signaling pathway / ruffle membrane / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / blood coagulation / glucose homeostasis / heart development / T cell receptor signaling pathway / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / 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 / Protein tyrosine phosphatase, catalytic domain motif ...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 / Receptor-type tyrosine-protein phosphatase eta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDebreczeni, J.E. / Barr, A.J. / Eswaran, J. / Ugochukwu, E. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
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.F. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionFeb 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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

Downloads & links

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Assembly

Deposited unit
A: HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0386
Polymers36,7671
Non-polymers2705
Water45025
1
A: HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
hetero molecules

A: HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
hetero molecules

A: HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,11318
Polymers110,3023
Non-polymers81115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area9100 Å2
ΔGint-212 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.060, 86.060, 119.540
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-2305-

NI

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Components

#1: Protein HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J / 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 / CD14 8 ANTIGEN


Mass: 36767.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 1019-1311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / 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.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.01M NICL2,0.1M TRIS PH 8.5, 1M LI2SO4,150 UL SITTING DROPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2006 / Details: MIRROS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→46.6 Å / Num. obs: 11491 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.76 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.25
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.18 / % possible all: 91.2

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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 2AHS

2ahs


Resolution: 2.5→63.25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 18.803 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 547 4.8 %RANDOM
Rwork0.201 ---
obs0.203 10857 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 5 25 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222193
X-RAY DIFFRACTIONr_bond_other_d0.0010.021418
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9262979
X-RAY DIFFRACTIONr_angle_other_deg0.91533440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14123.832107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.2290.2464
X-RAY DIFFRACTIONr_nbd_other0.1970.21358
X-RAY DIFFRACTIONr_nbtor_refined0.190.21049
X-RAY DIFFRACTIONr_nbtor_other0.0860.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4851.51374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84622159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1483947
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6834.5820
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 38
Rwork0.264 788
Refinement TLS params.Method: refined / Origin x: -7.054 Å / Origin y: 28.52 Å / Origin z: -14.381 Å
111213212223313233
T0.201 Å2-0.114 Å20.0393 Å2--0.1333 Å20.023 Å2---0.0929 Å2
L1.7566 °2-0.4098 °2-0.0498 °2-3.2916 °2-0.7789 °2--3.509 °2
S-0.1634 Å °-0.0701 Å °-0.275 Å °0.2248 Å °0.1076 Å °0.2215 Å °0.814 Å °-0.3864 Å °0.0558 Å °

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