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- PDB-6du2: Structure of Scp1 D96N bound to REST-pS861/4 peptide -

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Basic information

Entry
Database: PDB / ID: 6du2
TitleStructure of Scp1 D96N bound to REST-pS861/4 peptide
Components
  • REST-pS861/4
  • carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2
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 / modification of synaptic structure / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / RNA polymerase II CTD heptapeptide repeat phosphatase activity / 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 dense core granule biogenesis / negative regulation of amniotic stem cell differentiation / modification of synaptic structure / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / RNA polymerase II CTD heptapeptide repeat phosphatase activity / 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 / auditory receptor cell stereocilium organization / positive regulation of programmed cell death / nervous system process / cellular response to glucocorticoid stimulus / regulation of alternative mRNA splicing, via spliceosome / regulation of osteoblast differentiation / myosin phosphatase activity / protein-serine/threonine phosphatase / cellular response to stress / positive regulation of stem cell population maintenance / neuromuscular process controlling balance / somatic stem cell population maintenance / negative regulation by host of viral transcription / negative regulation of neuron differentiation / hematopoietic progenitor cell differentiation / negative regulation of insulin secretion / RNA polymerase II core promoter sequence-specific DNA binding / transcription repressor complex / positive regulation of neuron differentiation / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / response to ischemia / HDACs deacetylate histones / negative regulation of neurogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / positive regulation of apoptotic process / chromatin remodeling / 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 / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
REST-like, C2H2-type zinc finger / 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 / : / HAD superfamily/HAD-like ...REST-like, C2H2-type zinc finger / 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 / : / HAD superfamily/HAD-like / Zinc finger, C2H2 type / 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
protein-serine/threonine phosphatase / protein-serine/threonine phosphatase / RE1-silencing transcription factor
Similarity search - Component
Biological speciesErinaceus europaeus (western European hedgehog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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 isoform X2
B: carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2
C: REST-pS861/4
D: REST-pS861/4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4016
Polymers44,3524
Non-polymers492
Water18010
1
A: carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2
C: REST-pS861/4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2003
Polymers22,1762
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-22 kcal/mol
Surface area9180 Å2
MethodPISA
2
B: carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 isoform X2
D: REST-pS861/4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2003
Polymers22,1762
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-21 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.335, 78.568, 62.883
Angle α, β, γ (deg.)90.000, 112.130, 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 isoform X2


Mass: 20738.607 Da / Num. of mol.: 2 / Mutation: D96N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erinaceus europaeus (western European hedgehog)
Gene: CTDSP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S2ZIN9, UniProt: A0A1S2ZIM2*PLUS
#2: Protein/peptide REST-pS861/4


Mass: 1437.400 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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.14 %
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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19287 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Χ2: 1.24 / Net I/σ(I): 6.5 / Num. measured all: 70073
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.5430.4868150.848184.3
2.54-2.593.10.5288950.86192.5
2.59-2.643.30.4899280.966193.9
2.64-2.693.40.4499360.853198.7
2.69-2.753.60.4279850.954199.6
2.75-2.823.60.419640.9461100
2.82-2.893.80.3349740.9541100
2.89-2.963.80.30110120.9331100
2.96-3.053.80.2329550.9911100
3.05-3.153.80.1999671.0851100
3.15-3.263.80.1759721.1931100
3.26-3.393.80.1449731.211100
3.39-3.553.80.1249881.311100
3.55-3.733.80.1079761.451100
3.73-3.973.80.0929861.6361100
3.97-4.273.70.089741.8811100
4.27-4.73.70.0689871.8311100
4.7-5.383.70.0599801.4881100
5.38-6.783.70.0569991.1671100
6.78-503.70.04910211.824199.9

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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: 2.5→39.46 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs19286 98.5 %
Displacement parametersBiso max: 111.74 Å2 / Biso mean: 48.3851 Å2 / Biso min: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 2 10 3011

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