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- PDB-2l0i: Solution structure of Rtt103 CTD-interacting domain bound to a Se... -

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Basic information

Entry
Database: PDB / ID: 2l0i
TitleSolution structure of Rtt103 CTD-interacting domain bound to a Ser2 phosphorylated CTD peptide
Components
  • DNA-directed RNA polymerasePolymerase
  • Regulator of Ty1 transposition protein 103
KeywordsTRANSCRIPTION / 3' end processing
Function / homology
Function and homology information


RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / 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 / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes ...RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / 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 / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / Dual incision in TC-NER / RNA polymerase II complex binding / Gap-filling DNA repair synthesis and ligation in TC-NER / translesion synthesis / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / site of double-strand break / transcription by RNA polymerase II / chromatin / mitochondrion / DNA binding / metal ion binding / nucleus
Similarity search - Function
: / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 ...: / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / 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 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Regulator of Ty1 transposition protein 103
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLunde, B.M. / Reichow, S.L. / Kim, M. / Suh, H. / Leeper, T.C. / Yang, F. / Mutschler, H. / Buratowski, S. / Meinhart, A. / Varani, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.
Authors: Lunde, B.M. / Reichow, S.L. / Kim, M. / Suh, H. / Leeper, T.C. / Yang, F. / Mutschler, H. / Buratowski, S. / Meinhart, A. / Varani, G.
History
DepositionJul 6, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 103
B: DNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)18,1072
Polymers18,1072
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Regulator of Ty1 transposition protein 103


Mass: 16569.100 Da / Num. of mol.: 1 / Fragment: UNP residues 1-131 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTT103, YDR289C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05543
#2: Protein/peptide DNA-directed RNA polymerase / Polymerase


Mass: 1537.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C-terminal domain / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-13C NOESY
1413D 1H-15N NOESY
1513D (H)CCH-TOCSY
1612D 1H-1H NOESY
1712D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] Rtt103-1, 10 mM [U-99% 2H] TRIS-2, 120 mM sodium chloride-3, 1.5 mM CTD-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRtt103-1[U-98% 13C; U-98% 15N]1
10 mMTRIS-2[U-99% 2H]1
120 mMsodium chloride-31
1.5 mMCTD-41
Sample conditionsIonic strength: 0.120 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2HADDOCK -Bonvinstructure solution
CNS1.2HADDOCK -Bonvinrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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