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- PDB-6npw: SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide -

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Basic information

Entry
Database: PDB / ID: 6npw
TitleSSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide
Components
  • Ser2/Ser5 phosphorylated peptide
  • Ssu72 ortholog, LD40846p
  • Symplekin
KeywordsHYDROLASE / phosphatase / CTD of RNA pol II
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Transcription Termination / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage ...Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Transcription Termination / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / myosin phosphatase activity / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / : / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / protein-serine/threonine phosphatase / Formation of TC-NER Pre-Incision Complex / phosphatase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / Dual incision in TC-NER / RNA polymerase II activity / translesion synthesis / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-directed RNA polymerase / cytoplasmic stress granule / transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / metal ion binding / nucleus
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins ...Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins / Leucine-rich Repeat Variant / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Response regulator / Helix non-globular / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA-directed RNA polymerase II subunit RPB1 / Symplekin / RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Saccharomyces cerevisiae RM11-1a (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å
AuthorsIrani, S. / Zhang, Y.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription.
Authors: Irani, S. / Sipe, S.N. / Yang, W. / Burkholder, N.T. / Lin, B. / Sim, K. / Matthews, W.L. / Brodbelt, J.S. / Zhang, Y.
History
DepositionJan 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Symplekin
B: Ssu72 ortholog, LD40846p
C: Symplekin
D: Ssu72 ortholog, LD40846p
E: Ser2/Ser5 phosphorylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4856
Polymers123,3905
Non-polymers951
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.702, 127.702, 105.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Symplekin


Mass: 37495.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sym, CG2097 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8MSU4
#2: Protein Ssu72 ortholog, LD40846p


Mass: 23130.279 Da / Num. of mol.: 2 / Mutation: C13D, D144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ssu72, CG14216, Dmel_CG14216 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q9VWE4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, EC: 3.1.3.41
#3: Protein/peptide Ser2/Ser5 phosphorylated peptide


Mass: 2138.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae RM11-1a (yeast) / References: UniProt: P04050*PLUS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350 (w/v) and 100 mM HEPE pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.486→50 Å / Num. obs: 59967 / % possible obs: 100 % / Redundancy: 5 % / Net I/σ(I): 11.97
Reflection shellResolution: 2.49→2.55 Å / Num. unique obs: 4110

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IMI

4imi


Resolution: 2.486→48.943 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.83
RfactorNum. reflection% reflection
Rfree0.2349 2013 3.36 %
Rwork0.1892 --
obs0.1908 59967 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.486→48.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8237 0 5 210 8452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058352
X-RAY DIFFRACTIONf_angle_d0.69411259
X-RAY DIFFRACTIONf_dihedral_angle_d9.1695191
X-RAY DIFFRACTIONf_chiral_restr0.0421309
X-RAY DIFFRACTIONf_plane_restr0.0041456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4856-2.54780.34181410.26274110X-RAY DIFFRACTION100
2.5478-2.61670.27631430.22654114X-RAY DIFFRACTION100
2.6167-2.69360.28691410.21514114X-RAY DIFFRACTION100
2.6936-2.78060.27971450.21114147X-RAY DIFFRACTION100
2.7806-2.880.24061430.21354108X-RAY DIFFRACTION100
2.88-2.99520.23951450.21014086X-RAY DIFFRACTION100
2.9952-3.13150.27411440.21054168X-RAY DIFFRACTION100
3.1315-3.29660.25681490.20984115X-RAY DIFFRACTION100
3.2966-3.50310.24261410.19584120X-RAY DIFFRACTION100
3.5031-3.77350.24091410.18874161X-RAY DIFFRACTION100
3.7735-4.15310.2131450.18134137X-RAY DIFFRACTION100
4.1531-4.75360.21461430.16054171X-RAY DIFFRACTION100
4.7536-5.98730.22271460.18844157X-RAY DIFFRACTION100
5.9873-48.95270.19611460.15644246X-RAY DIFFRACTION100

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