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

Basic information

• Entry: Database: SASBDB / ID: SASDCZ2

Sample

Yeast 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 RPB1 (protein), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Function / homology

Function:

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

Domain/homology:

: / CID domain / RPR / CID domain / CID domain profile. / 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

Component:

DNA-directed RNA polymerase II subunit RPB1 / Regulator of Ty1 transposition protein 103

• Biological species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
• Citation: Date: 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)

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)

Sample

• Sample: Name: 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
• Buffer: Name: 25 mM KH2PO4, 300 mM KCl, 10 mM BME / pH: 6.5

Entity #615

Type: 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 FDKSSDELDP SSSVYEENFK TISKIGNMAK DIINESILKR ESGIHKLQST LDDEKRHLDE EQNMLSEIEF VLSAKDL

Entity #616

Type: protein / Description: DNA-directed RNA polymerase II subunit RPB1 / 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

Experimental information

• Beam: Instrument 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
• Detector: Name: 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 /

	Min	Max
Q	0.0037	0.6627

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 93 /

	Min	Max
Q	0.0180756	0.150167
P(R) point	1	93
R	0	210.5

Result

Type of curve: single_conc /

	Experimental	Porod
MW	184.5 kDa	350.625 kDa
Volume	-	561 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.1937	0.00423	0.18	0.0027
Radius of gyration, Rg	5.767 nm	0.014	5.294 nm	0.02

	Min	Max
D	-	21
Guinier point	7	15