[English] 日本語
Yorodumi
- PDB-1vhr: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vhr
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE
ComponentsHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
KeywordsHYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE
Function / homology
Function and homology information


MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / dephosphorylation ...MAP kinase phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / negative regulation of chemotaxis / negative regulation of T cell activation / positive regulation of focal adhesion disassembly / negative regulation of JNK cascade / ERKs are inactivated / regulation of focal adhesion assembly / negative regulation of T cell receptor signaling pathway / dephosphorylation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / phosphatase activity / peptidyl-tyrosine dephosphorylation / immunological synapse / negative regulation of MAPK cascade / cytoskeletal protein binding / cellular response to epidermal growth factor stimulus / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine kinase binding / protein tyrosine phosphatase activity / negative regulation of cell migration / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR SOFTWARE USED : PHASES STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 2.1 Å
AuthorsYuvaniyama, J. / Denu, J.M. / Dixon, J.E. / Saper, M.A.
Citation
Journal: Science / Year: 1996
Title: Crystal structure of the dual specificity protein phosphatase VHR.
Authors: Yuvaniyama, J. / Denu, J.M. / Dixon, J.E. / Saper, M.A.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: The Purification and Characterization of a Human Dual-Specific Protein Tyrosine Phosphatase
Authors: Denu, J.M. / Zhou, G. / Wu, L. / Zhao, R. / Yuvaniyama, J. / Saper, M.A. / Dixon, J.E.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: The Catalytic Role of Cys124 in the Dual Specificity Phosphatase Vhr
Authors: Zhou, G. / Denu, J.M. / Wu, L. / Dixon, J.E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Expression Cloning of a Human Dual-Specificity Phosphatase
Authors: Ishibashi, T. / Bottaro, D.P. / Chan, A. / Miki, T. / Aaronson, S.A.
History
DepositionFeb 20, 1996Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
B: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0754
Polymers40,7402
Non-polymers3342
Water2,540141
1
A: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6082
Polymers20,3701
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4662
Polymers20,3701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.148, 60.040, 52.016
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.962481, -0.060958, -0.264412), (-0.050633, 0.997671, -0.045694), (0.266582, -0.030591, -0.963327)
Vector: 28.16632, 29.73183, 25.95833)

-
Components

#1: Protein HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE VHR / VHR


Mass: 20370.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: ORIGINAL GENE GDB\:DUSP3; VHR, CHROMOSOME MAP POSITION 17Q21
Plasmid: PT7-7-VHR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51452, protein-tyrosine-phosphatase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: THE FULL-LENGTH VHR (RESIDUES 2 - 185) WAS CRYSTALLIZED AT A CONCENTRATION OF 5-6 MG/ML WITH 14% POLYETHYLENE GLYCOL 4000, 22.5 MM LITHIUM SULFATE, 50 MM HEPES PH 7.0, AND 0.05% BETA- ...Details: THE FULL-LENGTH VHR (RESIDUES 2 - 185) WAS CRYSTALLIZED AT A CONCENTRATION OF 5-6 MG/ML WITH 14% POLYETHYLENE GLYCOL 4000, 22.5 MM LITHIUM SULFATE, 50 MM HEPES PH 7.0, AND 0.05% BETA-MERCAPTOETHANOL IN A HANGING DROP OF 20 MICROLITERS. THE DROP WAS EQUILIBRATED AGAINST 1 ML OF TWICE THE CONCENTRATION OF PRECIPITANT SOLUTION AT 23 DEGREE CELSIUS., vapor diffusion - hanging drop, temperature 296K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlVHR1drop
210-15 %PEG40001drop
322 mM1dropLi2SO4
40.1 %beta-mercaptoethanol1drop
550 mMHEPES1drop
6precipitant1reservoirtwice the concentration

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 27, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→90 Å / Num. obs: 18952 / % possible obs: 86.4 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. measured all: 41078

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR SOFTWARE USED : PHASES STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.254 -9.96 %
Rwork0.176 --
obs0.176 18746 86.4 %
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 20 141 2929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.654
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.87
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.87

+
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