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- PDB-5lvf: Solution structure of Rtt103 CTD-interacting domain bound to a Th... -

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Basic information

Entry
Database: PDB / ID: 5lvf
TitleSolution structure of Rtt103 CTD-interacting domain bound to a Thr4 phosphorylated CTD peptide
Components
  • PRO-SER-TYR-SER-PRO-PTH-SER-PRO-SER-TYR-SER-PRO-THR-SER-PRO-SER
  • Regulator of Ty1 transposition protein 103
KeywordsTRANSCRIPTION / CTD-interacting domain / RNAPII CTD
Function / homology
Function and homology information


RNA polymerase II C-terminal domain phosphoserine binding / transposable element 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 / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA polymerase II C-terminal domain phosphoserine binding / transposable element 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 / RNA polymerase II transcribes snRNA genes / 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 Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / Estrogen-dependent gene expression / Dual incision in TC-NER / translesion synthesis / RNA polymerase II, core complex / : / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / : / : / : / : / : / : / DNA-directed RNA polymerase / cytoplasmic stress granule / site of double-strand break / transcription by RNA polymerase II / chromatin / mitochondrion / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. ...: / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / 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 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / molecular dynamics
AuthorsJasnovidova, O. / Kubicek, K. / Krejcikova, M. / Stefl, R.
Funding support Czech Republic, Belgium, 2items
OrganizationGrant numberCountry
Czech Science Foundation13-18344S Czech Republic
European Research Council (ERC)649030 Belgium
CitationJournal: EMBO Rep. / Year: 2017
Title: Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p.
Authors: Jasnovidova, O. / Krejcikova, M. / Kubicek, K. / Stefl, R.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: PRO-SER-TYR-SER-PRO-PTH-SER-PRO-SER-TYR-SER-PRO-THR-SER-PRO-SER


Theoretical massNumber of molelcules
Total (without water)18,2912
Polymers18,2912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1510 Å2
ΔGint-5 kcal/mol
Surface area8060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTT103, YDR289C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05543
#2: Protein/peptide PRO-SER-TYR-SER-PRO-PTH-SER-PRO-SER-TYR-SER-PRO-THR-SER-PRO-SER


Mass: 1721.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic33D 1H-13C NOESY aromatic
141isotropic34D (H)CCH TOCSY
151isotropic33D HNCA
161isotropic1F1-13C/15N-filtered NOESY-[13C,1H]-HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Rtt103 CID, 1.2 mM pThr4-CTD, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRtt103 CID[U-13C; U-15N]1
1.2 mMpThr4-CTDnatural abundance1
Sample conditionsDetails: 35mM KH2PO4 100mM KCl / Ionic strength: 100 mM / Label: sample_1 / pH: 6.8 / Pressure: 760 mmHg / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III7003

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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