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- SASDCZ2: Yeast CTDsome: transcription termination factor Rtt103p/C-termina... -

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Basic information

Entry
Database: SASBDB / ID: SASDCZ2
SampleYeast CTDsome: transcription termination factor Rtt103p/C-terminal domain of DNA-directed RNA polymerase II subunit RPB1 (Rtt103 1-246-phospho-mimetic complex)
  • Regulator of Ty1 transposition protein 103 (protein), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
  • DNA-directed RNA polymerase II subunit RPB1Polymerase (protein), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 / 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 / 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 / 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-templated transcription / RNA Polymerase II Pre-transcription Events / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / RNA polymerase II complex binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation 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 / 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. / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat ...: / CID domain / RPR / CID domain / CID domain profile. / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Regulator of Ty1 transposition protein 103
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
CitationDate: 2017 Oct 4
Title: Structure and dynamics of the RNAPII CTDsome with Rtt103
Authors: Jasnovidova O / Klumpler T / Kubicek K / Kalynych S / Plevka P
Contact author
  • Tomas Klumpler (CEITEC - Central European Institute of Technology, Masaryk University)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1182
Type: mix / Software: (05) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.79 / P-value: 0.545500
Search similar-shape structures of this assembly by Omokage search (details)
Model #1195
Type: mix / Software: (05) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.81 / P-value: 0.966400
Search similar-shape structures of this assembly by Omokage search (details)
Model #1197
Type: mix / Software: (05) / Radius of dummy atoms: 1.90 A / Chi-square value: 0.81 / P-value: 0.321000
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Yeast CTDsome: transcription termination factor Rtt103p/C-terminal domain of DNA-directed RNA polymerase II subunit RPB1 (Rtt103 1-246-phospho-mimetic complex)
Specimen concentration: 1 mg/ml / Entity id: 615 / 616
BufferName: 25 mM KH2PO4, 300 mM KCl, 10 mM BME / pH: 6.5
Entity #615Type: protein / Description: Regulator of Ty1 transposition protein 103 / Formula weight: 28.627 / Num. of mol.: 2
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q05543
Sequence: MPFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQQ AKGQKIIQFQ DSFGKVAAEV LGRINQEFPR DLKKKLSRVV NILKERNIFS KQVVNDIERS LKTESSPVEA LVLPQKLKDF AKDYEKLVKM HHNVCAMKMR ...Sequence:
MPFSSEQFTT KLNTLEDSQE SISSASKWLL LQYRDAPKVA EMWKEYMLRP SVNTRRKLLG LYLMNHVVQQ AKGQKIIQFQ DSFGKVAAEV LGRINQEFPR DLKKKLSRVV NILKERNIFS KQVVNDIERS LKTESSPVEA LVLPQKLKDF AKDYEKLVKM HHNVCAMKMR FDKSSDELDP SSSVYEENFK TISKIGNMAK DIINESILKR ESGIHKLQST LDDEKRHLDE EQNMLSEIEF VLSAKDL
Entity #616Type: protein
Description: DNA-directed RNA polymerase II subunit RPB1Polymerase
Formula weight: 12.782 / Num. of mol.: 1
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04050
Sequence:
SPEFTCEPTS PSYEPTSPSY EPTSPSYEPT SPSYEPTSPS YEPTSPSYEP TSPSYEPTSP SYEPTSPSYE PTSPSYEPTS PSYEPTSPSY EPTSPSYEPT SPSYEPAAAD YKDDDDK

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Experimental information

BeamInstrument name: CEITEC Rigaku BioSAXS-1000 / City: Brno / 国: Czech Republic / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.4806 mm
DetectorName: Pilatus 100K / Pixsize x: 172 mm
Scan
Title: Rtt103 1-246-phospho-mimetic complex / Measurement date: Apr 12, 2016 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 3600 sec. / Number of frames: 5 / Unit: 1/A /
MinMax
Q0.0037 0.6627
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 93 /
MinMax
Q0.0180756 0.150167
P(R) point1 93
R0 210.5
Result
Type of curve: single_conc /
ExperimentalPorod
MW184.5 kDa350.625 kDa
Volume-561 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.1937 0.00423 0.18 0.0027
Radius of gyration, Rg5.767 nm0.014 5.294 nm0.02

MinMax
D-21
Guinier point7 15

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