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- PDB-6r8i: PP4R3A EVH1 domain bound to FxxP motif -

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Basic information

Entry
Database: PDB / ID: 6r8i
TitlePP4R3A EVH1 domain bound to FxxP motif
Components
  • SER-LEU-PRO-PHE-THR-PHE-LYS-VAL-PRO-ALA-PRO-PRO-PRO-SER-LEU-PRO-PRO-SER
  • Serine/threonine-protein phosphatase 4 regulatory subunit 3A
KeywordsPEPTIDE BINDING PROTEIN / PP4 / PPP4R3A / PPP4R3B / PPP4R2 / PP4C / phosphatase / EVH1 domain / PPII polyproline helix
Function / homology
Function and homology information


microtubule organizing center / nuclear speck / nucleoplasm / cytosol
Similarity search - Function
Serine/threonine-protein phosphatase 4 regulatory subunit 3-like, central domain / Phosphatase 4 regulatory subunit 3 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 4 regulatory subunit 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.517 Å
AuthorsUeki, Y. / Kruse, T. / Weisser, M.B. / Sundell, G.N. / Yoo Larsen, M.S. / Lopez Mendez, B. / Jenkins, N.P. / Garvanska, D.H. / Cressey, L. / Zhang, G. ...Ueki, Y. / Kruse, T. / Weisser, M.B. / Sundell, G.N. / Yoo Larsen, M.S. / Lopez Mendez, B. / Jenkins, N.P. / Garvanska, D.H. / Cressey, L. / Zhang, G. / Davey, N. / Montoya, G. / Ivarsson, Y. / Kettenbach, A. / Nilsson, J.
Funding support Denmark, United States, Ireland, Switzerland, 10items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Danish Council for Independent Research8021-00101B Denmark
Novo Nordisk FoundationNNF18OC0053124 Denmark
Swedish Research Council2016-04965 Denmark
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119455, P20GM113132 United States
Science Foundation Ireland13/SIRG/2193 Ireland
Lundbeckfonden2017-3212 Denmark
Swiss National Science FoundationP2EZP3_178624 Switzerland
Novo Nordisk FoundationNNF0024386 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
CitationJournal: Mol.Cell / Year: 2019
Title: A Consensus Binding Motif for the PP4 Protein Phosphatase.
Authors: Ueki, Y. / Kruse, T. / Weisser, M.B. / Sundell, G.N. / Larsen, M.S.Y. / Mendez, B.L. / Jenkins, N.P. / Garvanska, D.H. / Cressey, L. / Zhang, G. / Davey, N. / Montoya, G. / Ivarsson, Y. / ...Authors: Ueki, Y. / Kruse, T. / Weisser, M.B. / Sundell, G.N. / Larsen, M.S.Y. / Mendez, B.L. / Jenkins, N.P. / Garvanska, D.H. / Cressey, L. / Zhang, G. / Davey, N. / Montoya, G. / Ivarsson, Y. / Kettenbach, A.N. / Nilsson, J.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _refine.pdbx_diffrn_id / _software.name
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 4 regulatory subunit 3A
B: SER-LEU-PRO-PHE-THR-PHE-LYS-VAL-PRO-ALA-PRO-PRO-PRO-SER-LEU-PRO-PRO-SER


Theoretical massNumber of molelcules
Total (without water)15,5252
Polymers15,5252
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-6 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.586, 60.586, 91.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine/threonine-protein phosphatase 4 regulatory subunit 3A / SMEK homolog 1


Mass: 13458.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal residue S0 (Serine) is a remainder from the introduced N-terminal TEV protease cleavage site and not part of the natural PP4R3A sequence. It is not visible in the structure. ...Details: N-terminal residue S0 (Serine) is a remainder from the introduced N-terminal TEV protease cleavage site and not part of the natural PP4R3A sequence. It is not visible in the structure. Residue D115 was built as an alanine due to badly visible side chain electron density. Residues 116 following are not visible in the structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP4R3A, KIAA2010, PP4R3A, SMEK1, MSTP033 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IN85
#2: Protein/peptide SER-LEU-PRO-PHE-THR-PHE-LYS-VAL-PRO-ALA-PRO-PRO-PRO-SER-LEU-PRO-PRO-SER


Mass: 2066.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: model peptide / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 M tri-sodium citrate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→42.84 Å / Num. obs: 50548 / % possible obs: 99.71 % / Redundancy: 7 % / Net I/σ(I): 22.8
Reflection shellResolution: 1.52→1.59 Å / Num. unique obs: 8189

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSF

4wsf


Resolution: 1.517→42.841 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 2535 5.02 %
Rwork0.1894 --
obs0.1905 50497 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.517→42.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 94 1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061125
X-RAY DIFFRACTIONf_angle_d0.9081539
X-RAY DIFFRACTIONf_dihedral_angle_d2.927898
X-RAY DIFFRACTIONf_chiral_restr0.057167
X-RAY DIFFRACTIONf_plane_restr0.006207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5166-1.54580.37921390.35962649X-RAY DIFFRACTION100
1.5458-1.57730.30331410.30722691X-RAY DIFFRACTION100
1.5773-1.61160.29781420.29812668X-RAY DIFFRACTION100
1.6116-1.64910.27351390.28042675X-RAY DIFFRACTION100
1.6491-1.69030.26751410.24932685X-RAY DIFFRACTION100
1.6903-1.7360.22611380.23382653X-RAY DIFFRACTION100
1.736-1.78710.2451390.23312696X-RAY DIFFRACTION100
1.7871-1.84480.22421320.20232579X-RAY DIFFRACTION97
1.8448-1.91070.20111430.20722657X-RAY DIFFRACTION100
1.9107-1.98730.19861420.19492668X-RAY DIFFRACTION100
1.9873-2.07770.23671430.1912689X-RAY DIFFRACTION100
2.0777-2.18720.20971420.19482658X-RAY DIFFRACTION100
2.1872-2.32430.19351430.18832675X-RAY DIFFRACTION100
2.3243-2.50370.22361460.20212670X-RAY DIFFRACTION100
2.5037-2.75560.23631440.19762661X-RAY DIFFRACTION99
2.7556-3.15420.2031370.18862662X-RAY DIFFRACTION100
3.1542-3.97360.16591410.16022674X-RAY DIFFRACTION100
3.9736-42.85790.22111430.16892652X-RAY DIFFRACTION99

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