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- PDB-6ntp: PTP1B Domain of PTP1B-LOV2 Chimera -

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Basic information

Entry
Database: PDB / ID: 6ntp
TitlePTP1B Domain of PTP1B-LOV2 Chimera
ComponentsTyrosine-protein phosphatase non-receptor type 1,NPH1-1
KeywordsHYDROLASE / Protein tyrosine phosphatase / protein phosphorylation / signaling / diabetes / obesity / cancer
Function / homology
Function and homology information


blue light photoreceptor activity / regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response ...blue light photoreceptor activity / regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / non-specific serine/threonine protein kinase / mitochondrial matrix / protein kinase activity / cadherin binding / phosphorylation / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Protein-tyrosine phosphatase, non-receptor type-1/2 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Protein-tyrosine phosphatase, non-receptor type-1/2 / 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 / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
non-specific serine/threonine protein kinase / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHongdusit, A. / Sankaran, B. / Zwart, P.H. / Fox, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CBET 1804897 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169-01 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Nat Commun / Year: 2020
Title: Minimally disruptive optical control of protein tyrosine phosphatase 1B.
Authors: Hongdusit, A. / Zwart, P.H. / Sankaran, B. / Fox, J.M.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 1,NPH1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1742
Polymers52,1501
Non-polymers241
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The crystals are green and, thus, contain the FMN cofactor of LOV2.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-3 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.254, 89.254, 105.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1,NPH1-1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 52150.102 Da / Num. of mol.: 1 / Fragment: residues 2-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Avena sativa (oats)
Gene: PTPN1, PTP1B, NPH1-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P18031, UniProt: O49003, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.89→52.87 Å / Num. obs: 39530 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rsym value: 0.025 / Net I/σ(I): 17.2
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 1936 / CC1/2: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.075 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a5j

3a5j


Resolution: 1.89→44.67 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.223 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21175 1947 5 %RANDOM
Rwork0.17922 ---
obs0.18073 37270 99.27 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.89→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 1 224 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132414
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172255
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.6473266
X-RAY DIFFRACTIONr_angle_other_deg1.291.585268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2922.059136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68415465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2271518
X-RAY DIFFRACTIONr_chiral_restr0.070.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0791.9221145
X-RAY DIFFRACTIONr_mcbond_other2.0591.9191144
X-RAY DIFFRACTIONr_mcangle_it3.1862.8651435
X-RAY DIFFRACTIONr_mcangle_other3.1922.871436
X-RAY DIFFRACTIONr_scbond_it3.0962.3291269
X-RAY DIFFRACTIONr_scbond_other3.0962.3321270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7083.3441821
X-RAY DIFFRACTIONr_long_range_B_refined7.79324.052688
X-RAY DIFFRACTIONr_long_range_B_other7.70823.2052640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 173 -
Rwork0.355 2642 -
obs--97.78 %
Refinement TLS params.Method: refined / Origin x: -36.354 Å / Origin y: 30.092 Å / Origin z: -2.352 Å
111213212223313233
T0.166 Å2-0.0777 Å2-0.0049 Å2-0.135 Å2-0.0032 Å2--0.0029 Å2
L1.2373 °20.2513 °2-0.0996 °2-2.5414 °20.6659 °2--2.3607 °2
S0.0473 Å °0.0123 Å °0.0238 Å °-0.0649 Å °-0.0693 Å °0.0787 Å °-0.1761 Å °-0.2013 Å °0.022 Å °

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