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- PDB-9dj9: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in distinct ... -

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Basic information

Entry
Database: PDB / ID: 9dj9
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) in distinct apo form
ComponentsDual specificity protein phosphatase 3
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


receptor signaling protein tyrosine kinase inhibitor activity / 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 / ERKs are inactivated / dephosphorylation / negative regulation of JNK cascade / regulation of focal adhesion assembly ...receptor signaling protein tyrosine kinase inhibitor activity / 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 / ERKs are inactivated / dephosphorylation / negative regulation of JNK cascade / regulation of focal adhesion assembly / motile cilium / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / negative regulation of epidermal growth factor receptor signaling pathway / protein serine/threonine phosphatase activity / phosphatase activity / peptidyl-tyrosine dephosphorylation / immunological synapse / cytoskeletal protein binding / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / cytoskeleton / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Dual specificity protein phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å
AuthorsKeedy, D.A. / Lemberikman, A.M. / Isiorho, E.A. / Aleshin, A.E. / Wu, J. / Lambert, L.J. / Cosford, N.D.P. / Tautz, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21 AI160161 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133769 United States
CitationJournal: Acs Omega / Year: 2025
Title: Fragment Screening Identifies Novel Allosteric Binders and Binding Sites in the VHR ( DUSP3 ) Phosphatase.
Authors: Wu, J. / Baranowski, M.R. / Aleshin, A.E. / Isiorho, E.A. / Lambert, L.J. / De Backer, L.J.S. / Han, Y.N. / Das, R. / Sheffler, D.J. / Bobkov, A.A. / Lemberikman, A.M. / Keedy, D.A. / Cosford, N.D.P. / Tautz, L.
History
DepositionSep 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 3


Theoretical massNumber of molelcules
Total (without water)20,9851
Polymers20,9851
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.227, 59.204, 43.195
Angle α, β, γ (deg.)90.000, 102.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dual specificity protein phosphatase 3 / Dual specificity protein phosphatase VHR / Vaccinia H1-related phosphatase / VHR


Mass: 20984.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP3, VHR / Production host: Escherichia coli (E. coli)
References: UniProt: P51452, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 26.7% (w/v) PEG-4000) and equilibrated against the precipitant solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.924→34.318 Å / Num. obs: 12987 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.091 / Rrim(I) all: 0.163 / Net I/σ(I): 5.7
Reflection shellResolution: 1.924→1.958 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.561 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 656 / CC1/2: 0.341 / Rpim(I) all: 1.042 / Rrim(I) all: 1.884 / % possible all: 98.8

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Processing

Software
NameVersionClassification
autoPROC1.0.5data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.924→34.318 Å / SU ML: 0.2646 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 667 5.15 %Random selection by Dimple
Rwork0.1898 12294 --
obs0.1922 12961 98.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.3 Å2
Refinement stepCycle: LAST / Resolution: 1.924→34.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 0 78 1462
LS refinement shellResolution: 1.924→2.411 Å
RfactorNum. reflection% reflection
Rwork0.2541 --
Rfree-334 5 %
obs--98.37 %

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