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- PDB-6du3: Structure of Scp1 D96N bound to REST-pS861/4 peptide -

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Basic information

Entry
Database: PDB / ID: 6du3
TitleStructure of Scp1 D96N bound to REST-pS861/4 peptide
Components
  • Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
  • REST-pS861
KeywordsHYDROLASE/PEPTIDE / Phosphatase / Transcription Factor / Phosphorylation / Neurogenesis / HYDROLASE / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


negative regulation of dense core granule biogenesis / negative regulation of amniotic stem cell differentiation / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of transcription regulatory region DNA binding / modification of synaptic structure / Regulation of NPAS4 gene transcription / cellular response to electrical stimulus / negative regulation of mesenchymal stem cell differentiation ...negative regulation of dense core granule biogenesis / negative regulation of amniotic stem cell differentiation / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of transcription regulatory region DNA binding / modification of synaptic structure / Regulation of NPAS4 gene transcription / cellular response to electrical stimulus / negative regulation of mesenchymal stem cell differentiation / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / neuronal stem cell population maintenance / NGF-stimulated transcription / nervous system process / cellular response to glucocorticoid stimulus / auditory receptor cell stereocilium organization / positive regulation of programmed cell death / regulation of alternative mRNA splicing, via spliceosome / regulation of osteoblast differentiation / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of stem cell population maintenance / protein-serine/threonine phosphatase / somatic stem cell population maintenance / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / neuromuscular process controlling balance / negative regulation of neuron differentiation / negative regulation of insulin secretion / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / hematopoietic progenitor cell differentiation / positive regulation of neuron differentiation / transcription repressor complex / protein dephosphorylation / negative regulation of miRNA transcription / negative regulation of protein phosphorylation / Regulation of PTEN gene transcription / response to ischemia / HDACs deacetylate histones / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of neurogenesis / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / response to hypoxia / transcription cis-regulatory region binding / chromatin remodeling / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Zinc finger, C2H2 type / HAD superfamily/HAD-like / zinc finger / Zinc finger C2H2 type domain profile. ...Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Zinc finger, C2H2 type / HAD superfamily/HAD-like / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RE1-silencing transcription factor / Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsBurkholder, N.T. / Mayfield, J.E. / Yu, X. / Irani, S. / Arce, D.K. / Jiang, F. / Matthews, W. / Xue, Y. / Zhang, Y.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM104896-01A1 United States
Robert A. Welch FoundationF-1778 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Phosphatase activity of small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST).
Authors: Burkholder, N.T. / Mayfield, J.E. / Yu, X. / Irani, S. / Arce, D.K. / Jiang, F. / Matthews, W.L. / Xue, Y. / Zhang, Y.J.
History
DepositionJun 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: REST-pS861
D: REST-pS861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2416
Polymers44,1924
Non-polymers492
Water32418
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: REST-pS861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1203
Polymers22,0962
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-22 kcal/mol
Surface area9210 Å2
MethodPISA
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
D: REST-pS861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1203
Polymers22,0962
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-22 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.414, 78.731, 63.001
Angle α, β, γ (deg.)90.000, 112.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 / Nuclear LIM interactor-interacting factor 3 / NLI-interacting factor 3 / Small C-terminal domain ...Nuclear LIM interactor-interacting factor 3 / NLI-interacting factor 3 / Small C-terminal domain phosphatase 1 / Small CTD phosphatase 1


Mass: 20738.607 Da / Num. of mol.: 2 / Mutation: D96N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF, SCP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9GZU7, protein-serine/threonine phosphatase
#2: Protein/peptide REST-pS861


Mass: 1357.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13127*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350 0.2 M Magnesium acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 17864 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Χ2: 0.795 / Net I/σ(I): 7.6 / Num. measured all: 66701
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.57-2.6130.3846900.587176.6
2.61-2.663.30.358980.583197.5
2.66-2.713.60.3698800.584199.2
2.71-2.773.80.3079010.611198.1
2.77-2.833.80.2938770.594199.5
2.83-2.893.90.2448910.669198.1
2.89-2.973.80.229140.651199.6
2.97-3.053.80.1818860.664198.7
3.05-3.143.80.1479060.715199.3
3.14-3.243.90.1258880.692199.3
3.24-3.353.80.1059190.792198.6
3.35-3.493.80.0859050.771199.5
3.49-3.653.80.0758910.866199.4
3.65-3.843.80.0639010.88199.2
3.84-4.083.80.0538980.881199.4
4.08-4.393.80.0489280.949199.5
4.39-4.843.70.0469031.051199.4
4.84-5.533.80.0519121.171199.7
5.53-6.973.60.0529301.033199.7
6.97-503.70.0319461.028199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→39.2 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs17864 98 %
Displacement parametersBiso max: 100.64 Å2 / Biso mean: 38.2103 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: LAST / Resolution: 2.58→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 2 18 3016

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