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UniProtKB/Swiss-Prot entry P04050

[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name RPB1_YEAST
Primary accession number P04050
Secondary accession numbers Q12364 Q92315
Integrated into Swiss-Prot on November 1, 1986
Sequence was last modified on November 1, 1997 (Sequence version 2)
Annotations were last modified on    November 4, 2008 (Entry version 107)
Name and origin of the protein
Protein name DNA-directed RNA polymerase II subunit RPB1
Synonyms RNA polymerase II subunit B1
RNA polymerase II subunit 1
EC 2.7.7.6
DNA-directed RNA polymerase III largest subunit
B220
Gene name
Name: RPB1
Synonyms: RPB220, RPO21, SUA8
OrderedLocusNames: YDL140C
ORFNames: D2150
From
Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932] 
Taxonomy Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
Protein existence 1: Evidence at protein level;
References
[1]
 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204626 / S288c / A364A;
DOI=10.1016/0092-8674(85)90117-5; PubMed=3896517 [NCBI, ExPASy, EBI, Israel, Japan]
Allison L.A., Moyle M., Shales M., Ingles C.J.;
"Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases.";
Cell 42:599-610(1985).
[2]
 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
DOI=10.1002/(SICI)1097-0061(199612)12:15<1549::AID-YEA42>3.3.CO;2-J; PubMed=8972577 [NCBI, ExPASy, EBI, Israel, Japan]
Woelfl S., Haneman V., Saluz H.P.;
"Analysis of a 26,756 bp segment from the left arm of yeast chromosome IV.";
Yeast 12:1549-1554(1996).
[3]
 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=9169867 [NCBI, ExPASy, EBI, Israel, Japan]
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[4]
 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1669-1733.
STRAIN=ATCC 204508 / S288c;
DOI=10.1016/0378-1097(95)00210-V; PubMed=7649444 [NCBI, ExPASy, EBI, Israel, Japan]
Cronan J.E. Jr., Wallace J.C.;
"The gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae.";
FEMS Microbiol. Lett. 130:221-230(1995).
[5]
 MUTAGENESIS OF THE CTD.
PubMed=7498765 [NCBI, ExPASy, EBI, Israel, Japan]
West M.L., Corden J.L.;
"Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations.";
Genetics 140:1223-1233(1995).
[6]
 PHOSPHORYLATION BY THE TFIIK COMPLEX AND THE SRB8-11 COMPLEX.
DOI=10.1016/S1097-2765(00)80112-4; PubMed=9702190 [NCBI, ExPASy, EBI, Israel, Japan]
Hengartner C.J., Myer V.E., Liao S.-M., Wilson C.J., Koh S.S., Young R.A.;
"Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases.";
Mol. Cell 2:43-53(1998).
[7]
 INTERACTION WITH ESS1.
DOI=10.1074/jbc.274.44.31583; PubMed=10531363 [NCBI, ExPASy, EBI, Israel, Japan]
Morris D.P., Phatnani H.P., Greenleaf A.L.;
"Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3'-End formation.";
J. Biol. Chem. 274:31583-31587(1999).
[8]
 DEPHOSPHORYLATION BY FCP1.
DOI=10.1016/S1097-2765(00)80187-2; PubMed=10445027 [NCBI, ExPASy, EBI, Israel, Japan]
Kobor M.S., Archambault J., Lester W., Holstege F.C.P., Gileadi O., Jansma D.B., Jennings E.G., Kouyoumdjian F., Davidson A.R., Young R.A., Greenblatt J.;
"An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae.";
Mol. Cell 4:55-62(1999).
[9]
 PHOSPHORYLATION BY THE BUR KINASE COMPLEX.
DOI=10.1128/MCB.21.13.4089-4096.2001; PubMed=11390638 [NCBI, ExPASy, EBI, Israel, Japan]
Murray S., Udupa R., Yao S., Hartzog G., Prelich G.;
"Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase.";
Mol. Cell. Biol. 21:4089-4096(2001).
[10]
 UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-695, AND MASS SPECTROMETRY.
DOI=10.1073/pnas.2135500100; PubMed=14557538 [NCBI, ExPASy, EBI, Israel, Japan]
Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.;
"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery.";
Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003).
[11]
 PHOSPHORYLATION BY CTD KINASE.
DOI=10.1074/jbc.M402218200; PubMed=15047695 [NCBI, ExPASy, EBI, Israel, Japan]
Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L.;
"C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats.";
J. Biol. Chem. 279:24957-24964(2004).
[12]
 INTERACTION WITH RTT103.
DOI=10.1038/nature03041; PubMed=15565157 [NCBI, ExPASy, EBI, Israel, Japan]
Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S.;
"The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.";
Nature 432:517-522(2004).
[13]
 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-621, AND MASS SPECTROMETRY.
DOI=10.1073/pnas.0701622104; PubMed=17563356 [NCBI, ExPASy, EBI, Israel, Japan]
Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.;
"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.";
Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007).
[14]
 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1471 AND TYR-1473, AND MASS SPECTROMETRY.
DOI=10.1074/mcp.M700468-MCP200; PubMed=18407956 [NCBI, ExPASy, EBI, Israel, Japan]
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[15]
 ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.
DOI=10.1016/S1097-2765(03)00387-3; PubMed=14580350 [NCBI, ExPASy, EBI, Israel, Japan]
Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J.;
"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex.";
Mol. Cell 12:1003-1013(2003).
[16]
 X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
DOI=10.1126/science.1059493; PubMed=11313498 [NCBI, ExPASy, EBI, Israel, Japan]
Cramer P., Bushnell D.A., Kornberg R.D.;
"Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution.";
Science 292:1863-1876(2001).
[17]
 X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
DOI=10.1126/science.1059495; PubMed=11313499 [NCBI, ExPASy, EBI, Israel, Japan]
Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D.;
"Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.";
Science 292:1876-1882(2001).
[18]
 X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN COMPLEX WITH ALPHA-AMANITIN.
DOI=10.1073/pnas.251664698; PubMed=11805306 [NCBI, ExPASy, EBI, Israel, Japan]
Bushnell D.A., Cramer P., Kornberg R.D.;
"Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution.";
Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002).
[19]
 X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
DOI=10.1016/S0092-8674(03)00598-1; PubMed=12914699 [NCBI, ExPASy, EBI, Israel, Japan]
Kettenberger H., Armache K.J., Cramer P.;
"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.";
Cell 114:347-357(2003).
[20]
 X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
DOI=10.1073/pnas.1030608100; PubMed=12746495 [NCBI, ExPASy, EBI, Israel, Japan]
Armache K.J., Kettenberger H., Cramer P.;
"Architecture of initiation-competent 12-subunit RNA polymerase II.";
Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003).
[21]
 X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
DOI=10.1073/pnas.1130601100; PubMed=12746498 [NCBI, ExPASy, EBI, Israel, Japan]
Bushnell D.A., Kornberg R.D.;
"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription.";
Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003).
[22]
 X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
DOI=10.1016/j.cell.2004.10.016; PubMed=15537538 [NCBI, ExPASy, EBI, Israel, Japan]
Westover K.D., Bushnell D.A., Kornberg R.D.;
"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.";
Cell 119:481-489(2004).
[23]
 X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
DOI=10.1016/j.molcel.2004.11.040; PubMed=15610738 [NCBI, ExPASy, EBI, Israel, Japan]
Kettenberger H., Armache K.J., Cramer P.;
"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.";
Mol. Cell 16:955-965(2004).
[24]
 X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
DOI=10.1126/science.1090838; PubMed=14963322 [NCBI, ExPASy, EBI, Israel, Japan]
Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D.;
"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms.";
Science 303:983-988(2004).
[25]
 X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
DOI=10.1074/jbc.M413038200; PubMed=15591044 [NCBI, ExPASy, EBI, Israel, Japan]
Armache K.J., Mitterweger S., Meinhart A., Cramer P.;
"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.";
J. Biol. Chem. 280:7131-7134(2005).
[26]
 X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
DOI=10.1038/nsmb1032; PubMed=16341226 [NCBI, ExPASy, EBI, Israel, Japan]
Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P.;
"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.";
Nat. Struct. Mol. Biol. 13:44-48(2006).
[27]
 X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
DOI=10.1016/j.str.2006.04.003; PubMed=16765890 [NCBI, ExPASy, EBI, Israel, Japan]
Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J.;
"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.";
Structure 14:973-982(2006).
Comments
  • FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA.
  • CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
  • SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Interacts with ESS1 and RTT103.
  • INTERACTION:
    P27692:SPT5; NbExp=1; IntAct=EBI-15760, EBI-17937;
  • SUBCELLULAR LOCATION: Nucleus.
  • PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapepdtide repeat. The phosphorylated form of Pol II appears to carry, on average, one phosphate per repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed. Phosphorylation at 'Ser-5' occurs in promoter-proximal regions in early elongation. Phosphorylation at 'Ser-2' predominates in regions more distal to the promoter and triggers binding of the 3' RNA processing machinery. CTD kinases include KIN28 (as part of the TFKII complex, a subcomplex of the TFIIH holo complex), SSN3/SRB10 (as part of the SRB8-11 complex, a module of the Mediator complex), CTK1 (as part of CTD kinase), and probably BUR1 (as part of the BUR1-BUR2 kinase complex). Phosphatases include FCP1 and SSU72.
  • MISCELLANEOUS: Mutagenesis experiments demonstrate that the minimum viable CTD contains eight consensus Y-S-P-T-S-P-[A-S-N-G] heptapeptide repeats. Identical and simultaneous substitutions in a number of consecutive repeats are lethal: 'Ser-2' -> 'Ala-2' (14 repeats), 'Ser-5' -> 'Ala-5' (15 repeats), '2-Ser-Pro-Thr-Ser-5'-> '2-Ala-Pro-Thr-Ala-5' (10 repeats), 'Ser-2'-> 'Glu-2' (15 repeats), 'Ser-5' -> 'Glu-5' (12 repeats), '2-Ser-Pro-3' -> '2-Pro-Ser-3' (15 repeats) and 'Tyr-1' -> 'Phe-1' (12 repeats).
  • MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucelotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
  • SIMILARITY: Belongs to the RNA polymerase beta' chain family.
  • SIMILARITY: Contains 1 C2H2-type zinc finger.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
X03128; CAA26904.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
X96876; CAA65619.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z74188; CAA98713.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
U27182; AAC49058.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR S67686; RNBY2L.
RefSeq NP_010141.1; -.
3D structure databases
PDB
1I3Q; X-ray; 3.10 A; A=1-1733.[ExPASy / RCSB / EBI]
1I50; X-ray; 2.80 A; A=1-1733.[ExPASy / RCSB / EBI]
1I6H; X-ray; 3.30 A; A=1-1733.[ExPASy / RCSB / EBI]
1K83; X-ray; 2.80 A; A=1-1733.[ExPASy / RCSB / EBI]
1NIK; X-ray; 4.10 A; A=1-1733.[ExPASy / RCSB / EBI]
1NT9; X-ray; 4.20 A; A=1-1733.[ExPASy / RCSB / EBI]
1PQV; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
1R5U; X-ray; 4.50 A; A=1-1733.[ExPASy / RCSB / EBI]
1R9S; X-ray; 4.25 A; A=1-1733.[ExPASy / RCSB / EBI]
1R9T; X-ray; 3.50 A; A=1-1733.[ExPASy / RCSB / EBI]
1SFO; X-ray; 3.61 A; A=1-1733.[ExPASy / RCSB / EBI]
1TWA; X-ray; 3.20 A; A=1-1733.[ExPASy / RCSB / EBI]
1TWC; X-ray; 3.00 A; A=1-1733.[ExPASy / RCSB / EBI]
1TWF; X-ray; 2.30 A; A=1-1733.[ExPASy / RCSB / EBI]
1TWG; X-ray; 3.30 A; A=1-1733.[ExPASy / RCSB / EBI]
1TWH; X-ray; 3.40 A; A=1-1733.[ExPASy / RCSB / EBI]
1WCM; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
1Y1V; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
1Y1W; X-ray; 4.00 A; A=1-1733.[ExPASy / RCSB / EBI]
1Y1Y; X-ray; 4.00 A; A=1-1733.[ExPASy / RCSB / EBI]
1Y77; X-ray; 4.50 A; A=1-1733.[ExPASy / RCSB / EBI]
2B63; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
2B8K; X-ray; 4.15 A; A=1-1733.[ExPASy / RCSB / EBI]
2E2H; X-ray; 3.95 A; A=1-1733.[ExPASy / RCSB / EBI]
2E2I; X-ray; 3.41 A; A=1-1733.[ExPASy / RCSB / EBI]
2E2J; X-ray; 3.50 A; A=1-1733.[ExPASy / RCSB / EBI]
2JA5; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
2JA6; X-ray; 4.00 A; A=1-1733.[ExPASy / RCSB / EBI]
2JA7; X-ray; 3.80 A; A/M=1-1733.[ExPASy / RCSB / EBI]
2JA8; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
2NVQ; X-ray; 2.90 A; A=1-1733.[ExPASy / RCSB / EBI]
2NVT; X-ray; 3.36 A; A=1-1733.[ExPASy / RCSB / EBI]
2NVX; X-ray; 3.60 A; A=1-1733.[ExPASy / RCSB / EBI]
2NVY; X-ray; 3.40 A; A=1-1733.[ExPASy / RCSB / EBI]
2NVZ; X-ray; 4.30 A; A=1-1733.[ExPASy / RCSB / EBI]
2R7Z; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
2R92; X-ray; 3.80 A; A=1-1733.[ExPASy / RCSB / EBI]
2R93; X-ray; 4.00 A; A=1-1733.[ExPASy / RCSB / EBI]
2VUM; X-ray; 3.40 A; A=1-1733.[ExPASy / RCSB / EBI]
2YU9; X-ray; 3.40 A; A=1-1733.[ExPASy / RCSB / EBI]
Detailed list of linked structures.
PDBsum 1I3Q; -.
1I50; -.
1I6H; -.
1K83; -.
1NIK; -.
1NT9; -.
1PQV; -.
1R5U; -.
1R9S; -.
1R9T; -.
1SFO; -.
1TWA; -.
1TWC; -.
1TWF; -.
1TWG; -.
1TWH; -.
1WCM; -.
1Y1V; -.
1Y1W; -.
1Y1Y; -.
1Y77; -.
2B63; -.
2B8K; -.
2E2H; -.
2E2I; -.
2E2J; -.
2JA5; -.
2JA6; -.
2JA7; -.
2JA8; -.
2NVQ; -.
2NVT; -.
2NVX; -.
2NVY; -.
2NVZ; -.
2R7Z; -.
2R92; -.
2R93; -.
2VUM; -.
2YU9; -.
ModBase P04050.
Protein-protein interaction databases
DIP DIP:611N; -.
IntAct P04050; -.
Organism-specific databases
CYGD YDL140c; -.
SGD S000002299; RPO21.
Yeast-GFP YDL140C.
Gene expression databases
ArrayExpress P04050; -.
GermOnline YDL140C; Saccharomyces cerevisiae.
Ontologies
GO
GO:0005665; Cellular component: DNA-directed RNA polymerase II, core complex (traceable author statement from SGD).
GO:0005739; Cellular component: mitochondrion (inferred from direct assay from SGD).
GO:0003899; Molecular function: DNA-directed RNA polymerase activity (traceable author statement from SGD).
GO:0005515; Molecular function: protein binding (inferred from physical interaction from IntAct).
GO:0006366; Biological process: transcription from RNA polymerase II promoter (traceable author statement from SGD).
QuickGo view.
Family and domain databases
InterPro IPR000722; RNA_pol_A.
IPR000684; RNA_pol_II_repeat_euk.
IPR006592; RNA_pol_N.
IPR007080; RNA_pol_Rpb1_1.
IPR007066; RNA_pol_Rpb1_3.
IPR007083; RNA_pol_Rpb1_4.
IPR007081; RNA_pol_Rpb1_5.
IPR007075; RNA_pol_Rpb1_6.
IPR007073; RNA_pol_Rpb1_7.
Graphical view of domain structure.
Gene3D G3DSA:2.40.40.30; RNA_pol_A; 1.
G3DSA:3.90.1120.10; RNA_pol_Rpb1_1; 1.
G3DSA:3.30.1360.90; RNA_pol_Rpb1_7; 1.
Pfam PF04997; RNA_pol_Rpb1_1; 1.
PF00623; RNA_pol_Rpb1_2; 1.
PF04983; RNA_pol_Rpb1_3; 1.
PF05000; RNA_pol_Rpb1_4; 1.
PF04998; RNA_pol_Rpb1_5; 1.
PF04992; RNA_pol_Rpb1_6; 1.
PF04990; RNA_pol_Rpb1_7; 1.
PF05001; RNA_pol_Rpb1_R; 14.
Pfam graphical view of domain structure.
SMART SM00663; RPOLA_N; 1.
SMART graphical view of domain structure.
PROSITE PS00115; RNA_POL_II_REPEAT; 22.
BLOCKS P04050.
ProtoNet P04050.
Proteomic databases
PeptideAtlas P04050; -.
Genome annotation databases
Ensembl YDL140C; Saccharomyces cerevisiae. [Contig view]
GeneID 851415; -.
GenomeReviews Z71256_GR; YDL140C.
KEGG sce:YDL140C; -.
NMPDR fig|4932.3.peg.878; -.
Phylogenomic databases
HOGENOM P04050; -.
Other
LinkHub P04050; -.
NextBio 968606; -.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Complete proteome; DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein; Repeat; Transcription; Transferase; Ubl conjugation; Zinc; Zinc-finger.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom    To Length Description FTId
CHAIN   1   1733  1733     DNA-directed RNA polymerase II subunit RPB1. PRO_0000073946
REPEAT   1549   1555  7     1. 
REPEAT   1556   1562  7     2. 
REPEAT   1563   1569  7     3. 
REPEAT   1570   1576  7     4. 
REPEAT   1577   1583  7     5. 
REPEAT   1584   1590  7     6. 
REPEAT   1591   1597  7     7. 
REPEAT   1598   1604  7     8. 
REPEAT   1605   1611  7     9. 
REPEAT   1612   1618  7     10. 
REPEAT   1619   1625  7     11. 
REPEAT   1626   1632  7     12. 
REPEAT   1633   1639  7     13. 
REPEAT   1640   1646  7     14. 
REPEAT   1647   1653  7     15. 
REPEAT   1654   1660  7     16. 
REPEAT   1661   1667  7     17. 
REPEAT   1668   1674  7     18. 
REPEAT   1675   1681  7     19. 
REPEAT   1682   1688  7     20. 
REPEAT   1689   1695  7     21. 
REPEAT   1696   1702  7     22. 
REPEAT   1703   1709  7     23. 
REPEAT   1710   1716  7     24; approximate. 
ZN_FING   67     83  17     C2H2-type. 
REGION   248    260  13     Lid loop. 
REGION   306    323  18     Rudder loop. 
REGION   810    822  13     Bridging helix. 
REGION   1549   1716  168     24 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[A-S-N-G]. 
METAL   67     67        Zinc 1. 
METAL   70     70        Zinc 1. 
METAL   77     77        Zinc 1. 
METAL   80     80        Zinc 1. 
METAL   107    107        Zinc 2. 
METAL   110    110        Zinc 2. 
METAL   148    148        Zinc 2. 
METAL   167    167        Zinc 2. 
METAL   481    481        Magnesium 1; catalytic. 
METAL   481    481        Magnesium 2; shared with RPB2. 
METAL   483    483        Magnesium 1; catalytic. 
METAL   483    483        Magnesium 2; shared with RPB2. 
METAL   485    485        Magnesium 1; catalytic. 
MOD_RES   621    621        Phosphothreonine. 
MOD_RES   1471   1471        Phosphothreonine. 
MOD_RES