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- PDB-8tk5: HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8tk5
TitleHUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with HEPES
ComponentsDual specificity protein phosphatase 3
KeywordsHYDROLASE / PROTEIN DUAL-SPECIFICITY PHOSPHATASE / VHR
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 / motile cilium / regulation of focal adhesion assembly / 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 / motile cilium / regulation of focal adhesion assembly / dephosphorylation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of T cell receptor signaling pathway / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase 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 / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to epidermal growth factor stimulus / positive regulation of mitotic cell cycle / protein tyrosine kinase binding / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytoskeleton / 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 / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Dual specificity protein phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAleshin, A.E. / Wu, J. / Lambert, L.J. / Cosford, N.D.P. / Tautz, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21 AI160161 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
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 3
B: Dual specificity protein phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8208
Polymers40,5662
Non-polymers1,2546
Water4,234235
1
A: Dual specificity protein phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0864
Polymers20,2831
Non-polymers8033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7344
Polymers20,2831
Non-polymers4513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.420, 59.250, 60.286
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 20283.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP3, VHR / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P51452, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.2 Å3/Da / Density % sol: 44.02 %
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 HEPES pH7.5, 50 mM NH4F, 28% (w/v) PEG 4K) and equilibrated against the precipitant solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→38.2 Å / Num. obs: 27321 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.157 / Num. unique obs: 1565 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.855 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19124 1631 6 %RANDOM
Rwork0.14695 ---
obs0.1496 25672 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.955 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å2-1.34 Å2
2---0.34 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 79 235 3136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123075
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162968
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6444151
X-RAY DIFFRACTIONr_angle_other_deg0.4761.576835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.085523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81910533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
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_it2.0451.7931519
X-RAY DIFFRACTIONr_mcbond_other2.031.7931519
X-RAY DIFFRACTIONr_mcangle_it3.0593.21918
X-RAY DIFFRACTIONr_mcangle_other3.0583.2031919
X-RAY DIFFRACTIONr_scbond_it3.2782.3171556
X-RAY DIFFRACTIONr_scbond_other3.2772.3181557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.21442234
X-RAY DIFFRACTIONr_long_range_B_refined6.59321.463461
X-RAY DIFFRACTIONr_long_range_B_other6.52920.533413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 115 -
Rwork0.173 1695 -
obs--87.78 %

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