[English] 日本語
Yorodumi
- PDB-8u1e: Apo protein tyrosine phosphatase 1B (PTP1B) at high resolution (1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u1e
TitleApo protein tyrosine phosphatase 1B (PTP1B) at high resolution (1.43 A) in space group P43212 with two distinctly ordered chains
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / Highest resolution apo-PTP1B structure
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / protein dephosphorylation / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSharma, S. / Mehlman, S.T. / Keedy, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH R35GM133769 United States
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2024
Title: High-resolution double vision of the allosteric phosphatase PTP1B.
Authors: Sharma, S. / Skaist Mehlman, T. / Sagabala, R.S. / Boivin, B. / Keedy, D.A.
#1: Journal: Biorxiv / Year: 2023
Title: High-resolution double vision of the archetypal protein tyrosine phosphatase
Authors: Sharma, S. / Mehlman, S.T. / Keedy, D.A.
History
DepositionAug 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1854
Polymers77,1362
Non-polymers492
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.412, 88.412, 163.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

-
Components

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


Mass: 38567.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18031
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MgCl2, 0.1 M Hepes pH 7.0, 15% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.43→30.59 Å / Num. obs: 119377 / % possible obs: 97.94 % / Redundancy: 25.6 % / Biso Wilson estimate: 24.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.029 / Rrim(I) all: 0.15 / Net I/σ(I): 10.82
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 25.7 % / Rmerge(I) obs: 9.777 / Mean I/σ(I) obs: 0.31 / Num. unique obs: 11763 / CC1/2: 0.404 / Rpim(I) all: 1.955 / Rrim(I) all: 9.974 / % possible all: 85.28

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS3.71data reduction
DIALS3.7.1data scaling
Coot0.9.8.2model building
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→30.59 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 5855 5 %
Rwork0.1497 111181 -
obs0.1523 117036 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.72 Å2
Refinement stepCycle: LAST / Resolution: 1.43→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 2 389 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00985214
X-RAY DIFFRACTIONf_angle_d1.0417093
X-RAY DIFFRACTIONf_chiral_restr0.0794743
X-RAY DIFFRACTIONf_plane_restr0.0108936
X-RAY DIFFRACTIONf_dihedral_angle_d5.5737726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.41671340.36063011X-RAY DIFFRACTION80.46
1.45-1.460.39521570.36223148X-RAY DIFFRACTION84.29
1.46-1.480.3731890.33543393X-RAY DIFFRACTION91.1
1.48-1.50.36281890.31593538X-RAY DIFFRACTION94.43
1.5-1.520.31682100.30333580X-RAY DIFFRACTION96.27
1.52-1.540.34571840.2873603X-RAY DIFFRACTION97.23
1.54-1.560.32482080.25913672X-RAY DIFFRACTION97.73
1.56-1.590.33772130.24813631X-RAY DIFFRACTION98.44
1.59-1.610.28271990.21433750X-RAY DIFFRACTION99.97
1.61-1.640.28211970.2043741X-RAY DIFFRACTION99.97
1.64-1.670.23991970.20173771X-RAY DIFFRACTION100
1.67-1.70.25771920.20033751X-RAY DIFFRACTION100
1.7-1.730.26121850.19683741X-RAY DIFFRACTION100
1.73-1.760.28992080.20343739X-RAY DIFFRACTION99.97
1.76-1.80.29631640.19643790X-RAY DIFFRACTION100
1.8-1.840.21722120.16193756X-RAY DIFFRACTION99.82
1.84-1.890.18871840.14313729X-RAY DIFFRACTION99.54
1.89-1.940.20522290.13353749X-RAY DIFFRACTION100
1.94-20.21131830.13013789X-RAY DIFFRACTION100
2-2.060.20252010.13543771X-RAY DIFFRACTION99.97
2.06-2.140.19971840.13693779X-RAY DIFFRACTION100
2.14-2.220.17742090.12633775X-RAY DIFFRACTION100
2.22-2.320.16832150.11913796X-RAY DIFFRACTION100
2.32-2.440.20141940.123782X-RAY DIFFRACTION99.57
2.44-2.60.17721970.12333823X-RAY DIFFRACTION100
2.6-2.80.21022070.14123813X-RAY DIFFRACTION100
2.8-3.080.22191900.14623857X-RAY DIFFRACTION99.98
3.08-3.520.19132100.1463860X-RAY DIFFRACTION99.73
3.53-4.440.15011940.12683940X-RAY DIFFRACTION100
4.44-30.590.18962200.14944103X-RAY DIFFRACTION99.49

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more