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P04050 (RPB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 154. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-directed RNA polymerase II subunit RPB1
Short name=RNA polymerase II subunit 1
Short name=RNA polymerase II subunit B1
EC=2.7.7.6
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
RNA polymerase II subunit B220
Gene names
Name:RPO21
Synonyms:RPB1, RPB220, SUA8
Ordered Locus Names:YDL140C
ORF Names:D2150
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length1733 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (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 structure

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Interacts with ASK10, ESS1, RTT103 and SHE2. Ref.8 Ref.11 Ref.14 Ref.17

Subcellular location

Nucleus.

Post-translational modification

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. Ref.7 Ref.9 Ref.10 Ref.13

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).

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 nucleotide 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.

Sequence similarities

Belongs to the RNA polymerase beta' chain family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

SEN1Q004163EBI-15760,EBI-16945
SPT5P276923EBI-15760,EBI-17937

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17331733DNA-directed RNA polymerase II subunit RPB1
PRO_0000073946

Regions

Repeat1549 – 155571
Repeat1556 – 156272
Repeat1563 – 156973
Repeat1570 – 157674
Repeat1577 – 158375
Repeat1584 – 159076
Repeat1591 – 159777
Repeat1598 – 160478
Repeat1605 – 161179
Repeat1612 – 1618710
Repeat1619 – 1625711
Repeat1626 – 1632712
Repeat1633 – 1639713
Repeat1640 – 1646714
Repeat1647 – 1653715
Repeat1654 – 1660716
Repeat1661 – 1667717
Repeat1668 – 1674718
Repeat1675 – 1681719
Repeat1682 – 1688720
Repeat1689 – 1695721
Repeat1696 – 1702722
Repeat1703 – 1709723
Repeat1710 – 1716724; approximate
Region248 – 26013Lid loop
Region306 – 32318Rudder loop
Region810 – 82213Bridging helix
Region1549 – 171616824 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[A-S-N-G]

Sites

Metal binding671Zinc 1
Metal binding701Zinc 1
Metal binding771Zinc 1
Metal binding801Zinc 1
Metal binding1071Zinc 2
Metal binding1101Zinc 2
Metal binding1481Zinc 2
Metal binding1671Zinc 2
Metal binding4811Magnesium 1; catalytic
Metal binding4811Magnesium 2; shared with RPB2
Metal binding4831Magnesium 1; catalytic
Metal binding4831Magnesium 2; shared with RPB2
Metal binding4851Magnesium 1; catalytic

Amino acid modifications

Modified residue6211Phosphothreonine Ref.15
Modified residue14711Phosphothreonine Ref.16
Modified residue14731Phosphotyrosine Ref.16
Cross-link695Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.12

Natural variations

Natural variant1653 – 16597Missing in strain: A364A.

Experimental info

Sequence conflict15141A → V in CAA26904. Ref.1
Sequence conflict15241G → A in CAA26904. Ref.1
Sequence conflict16011T → M Ref.1

Secondary structure

1 ..................................................................................................................................................................................................................................................................................................... 1733
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04050 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: A45C1360FF99F968

FASTA1,733191,612
        10         20         30         40         50         60 
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS 

        70         80         90        100        110        120 
IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE 

       130        140        150        160        170        180 
LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK 

       190        200        210        220        230        240 
LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP 

       250        260        270        280        290        300 
VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV 

       310        320        330        340        350        360 
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE 

       370        380        390        400        410        420 
LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDSG DRIDLRYSKR 

       430        440        450        460        470        480 
AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA 

       490        500        510        520        530        540 
DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF 

       550        560        570        580        590        600 
IELDQVLNML YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP 

       610        620        630        640        650        660 
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ KVVNFWLLHN 

       670        680        690        700        710        720 
GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR 

       730        740        750        760        770        780 
FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV 

       790        800        810        820        830        840 
DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR 

       850        860        870        880        890        900 
LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD 

       910        920        930        940        950        960 
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI 

       970        980        990       1000       1010       1020 
RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC 

      1030       1040       1050       1060       1070       1080 
LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT 

      1090       1100       1110       1120       1130       1140 
LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH 

      1150       1160       1170       1180       1190       1200 
TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA 

      1210       1220       1230       1240       1250       1260 
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML 

      1270       1280       1290       1300       1310       1320 
KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP 

      1330       1340       1350       1360       1370       1380 
GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG SYVNYRHMAL LVDVMTTQGG 

      1390       1400       1410       1420       1430       1440 
LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA 

      1450       1460       1470       1480       1490       1500 
FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS 

      1510       1520       1530       1540       1550       1560 
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS 

      1570       1580       1590       1600       1610       1620 
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS 

      1630       1640       1650       1660       1670       1680 
PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP 

      1690       1700       1710       1720       1730 
SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR

« Hide

References

« Hide 'large scale' references
[1]"Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases."
Allison L.A., Moyle M., Shales M., Ingles C.J.
Cell 42:599-610(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204626 / S288c / A364A.
[2]"Analysis of a 26,756 bp segment from the left arm of yeast chromosome IV."
Woelfl S., Haneman V., Saluz H.P.
Yeast 12:1549-1554(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
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. expand/collapse author list , 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.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"The gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae."
Cronan J.E. Jr., Wallace J.C.
FEMS Microbiol. Lett. 130:221-230(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1669-1733.
Strain: ATCC 204508 / S288c.
[6]"Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations."
West M.L., Corden J.L.
Genetics 140:1223-1233(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF THE CTD.
[7]"Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases."
Hengartner C.J., Myer V.E., Liao S.-M., Wilson C.J., Koh S.S., Young R.A.
Mol. Cell 2:43-53(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION BY THE TFIIK COMPLEX AND THE SRB8-11 COMPLEX.
[8]"Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3'-End formation."
Morris D.P., Phatnani H.P., Greenleaf A.L.
J. Biol. Chem. 274:31583-31587(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ESS1.
[9]"An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae."
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.
Mol. Cell 4:55-62(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: DEPHOSPHORYLATION BY FCP1.
[10]"Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase."
Murray S., Udupa R., Yao S., Hartzog G., Prelich G.
Mol. Cell. Biol. 21:4089-4096(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION BY THE BUR KINASE COMPLEX.
[11]"Ask10p mediates the oxidative stress-induced destruction of the Saccharomyces cerevisiae C-type cyclin Ume3p/Srb11p."
Cohen T.J., Lee K., Rutkowski L.H., Strich R.
Eukaryot. Cell 2:962-970(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ASK10.
[12]"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-695, MASS SPECTROMETRY.
[13]"C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats."
Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L.
J. Biol. Chem. 279:24957-24964(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION BY CTD KINASE.
[14]"The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II."
Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S.
Nature 432:517-522(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RTT103.
[15]"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases."
Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.
Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-621, MASS SPECTROMETRY.
[16]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1471 AND TYR-1473, MASS SPECTROMETRY.
[17]"Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud."
Shen Z., St-Denis A., Chartrand P.
Genes Dev. 24:1914-1926(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SHE2.
[18]"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex."
Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J.
Mol. Cell 12:1003-1013(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.
[19]"Structural basis of transcription: RNA polymerase II at 2.8 A resolution."
Cramer P., Bushnell D.A., Kornberg R.D.
Science 292:1863-1876(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[20]"Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution."
Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D.
Science 292:1876-1882(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[21]"Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution."
Bushnell D.A., Cramer P., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN COMPLEX WITH ALPHA-AMANITIN.
[22]"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage."
Kettenberger H., Armache K.J., Cramer P.
Cell 114:347-357(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
[23]"Architecture of initiation-competent 12-subunit RNA polymerase II."
Armache K.J., Kettenberger H., Cramer P.
Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
[24]"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription."
Bushnell D.A., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[25]"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center."
Westover K.D., Bushnell D.A., Kornberg R.D.
Cell 119:481-489(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[26]"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS."
Kettenberger H., Armache K.J., Cramer P.
Mol. Cell 16:955-965(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
[27]"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms."
Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D.
Science 303:983-988(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[28]"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7."
Armache K.J., Mitterweger S., Meinhart A., Cramer P.
J. Biol. Chem. 280:7131-7134(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
[29]"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs."
Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P.
Nat. Struct. Mol. Biol. 13:44-48(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
[30]"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model."
Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J.
Structure 14:973-982(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X03128 Genomic DNA. Translation: CAA26904.1.
X96876 Genomic DNA. Translation: CAA65619.1.
Z74188 Genomic DNA. Translation: CAA98713.1.
U27182 Genomic DNA. Translation: AAC49058.1.
BK006938 Genomic DNA. Translation: DAA11718.1.
PIRRNBY2L. S67686.
RefSeqNP_010141.1. NM_001180200.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10A1-1733[»]
1I50X-ray2.80A1-1733[»]
1I6HX-ray3.30A1-1733[»]
1K83X-ray2.80A1-1733[»]
1NIKX-ray4.10A1-1733[»]
1NT9X-ray4.20A1-1733[»]
1PQVX-ray3.80A1-1733[»]
1R5UX-ray4.50A1-1733[»]
1R9SX-ray4.25A1-1733[»]
1R9TX-ray3.50A1-1733[»]
1SFOX-ray3.61A1-1733[»]
1TWAX-ray3.20A1-1733[»]
1TWCX-ray3.00A1-1733[»]
1TWFX-ray2.30A1-1733[»]
1TWGX-ray3.30A1-1733[»]
1TWHX-ray3.40A1-1733[»]
1WCMX-ray3.80A1-1733[»]
1Y1VX-ray3.80A1-1733[»]
1Y1WX-ray4.00A1-1733[»]
1Y1YX-ray4.00A1-1733[»]
1Y77X-ray4.50A1-1733[»]
2B63X-ray3.80A1-1733[»]
2B8KX-ray4.15A1-1733[»]
2E2HX-ray3.95A1-1733[»]
2E2IX-ray3.41A1-1733[»]
2E2JX-ray3.50A1-1733[»]
2JA5X-ray3.80A1-1733[»]
2JA6X-ray4.00A1-1733[»]
2JA7X-ray3.80A/M1-1733[»]
2JA8X-ray3.80A1-1733[»]
2L0INMR-B1556-1569[»]
2LO6NMR-B1556-1569[»]
2NVQX-ray2.90A1-1733[»]
2NVTX-ray3.36A1-1733[»]
2NVXX-ray3.60A1-1733[»]
2NVYX-ray3.40A1-1733[»]
2NVZX-ray4.30A1-1733[»]
2R7ZX-ray3.80A1-1733[»]
2R92X-ray3.80A1-1733[»]
2R93X-ray4.00A1-1733[»]
2VUMX-ray3.40A1-1733[»]
2YU9X-ray3.40A1-1733[»]
3CQZX-ray2.80A1-1733[»]
3FKIX-ray3.88A1-1733[»]
3GTGX-ray3.78A1-1733[»]
3GTJX-ray3.42A1-1733[»]
3GTKX-ray3.80A1-1733[»]
3GTLX-ray3.38A1-1733[»]
3GTMX-ray3.80A1-1733[»]
3GTOX-ray4.00A1-1733[»]
3GTPX-ray3.90A1-1733[»]
3GTQX-ray3.80A1-1733[»]
3H3VX-ray4.00B1-1733[»]
3HOUX-ray3.20A/M1-1733[»]
3HOVX-ray3.50A1-1733[»]
3HOWX-ray3.60A1-1733[»]
3HOXX-ray3.65A1-1733[»]
3HOYX-ray3.40A1-1733[»]
3HOZX-ray3.65A1-1733[»]
3I4MX-ray3.70A1-1733[»]
3I4NX-ray3.90A1-1733[»]
3J1Nelectron microscopy16.00A1-1455[»]
3K1FX-ray4.30A1-1733[»]
3K7AX-ray3.80A1-1733[»]
3M3YX-ray3.18A1-1733[»]
3M4OX-ray3.57A1-1733[»]
3PO2X-ray3.30A1-1733[»]
3PO3X-ray3.30A1-1733[»]
3QT1X-ray4.30A1-1733[»]
3RZDX-ray3.30A1-1733[»]
3RZOX-ray3.00A1-1733[»]
3S14X-ray2.85A1-1733[»]
3S15X-ray3.30A1-1733[»]
3S16X-ray3.24A1-1733[»]
3S17X-ray3.20A1-1733[»]
3S1MX-ray3.13A1-1733[»]
3S1NX-ray3.10A1-1733[»]
3S1QX-ray3.30A1-1733[»]
3S1RX-ray3.20A1-1733[»]
3S2DX-ray3.20A1-1733[»]
3S2HX-ray3.30A1-1733[»]
4A3BX-ray3.50A1-1732[»]
4A3CX-ray3.50A1-1732[»]
4A3DX-ray3.40A1-1732[»]
4A3EX-ray3.40A1-1732[»]
4A3FX-ray3.50A1-1732[»]
4A3GX-ray3.50A1-1732[»]
4A3IX-ray3.80A1-1732[»]
4A3JX-ray3.70A1-1732[»]
4A3KX-ray3.50A1-1732[»]
4A3LX-ray3.50A1-1732[»]
4A3MX-ray3.90A1-1732[»]
4A93X-ray3.40A1-1732[»]
4BBRX-ray3.40A1-1733[»]
4BBSX-ray3.60A1-1733[»]
4GWQX-ray4.50H1556-1590[»]
ProteinModelPortalP04050.
SMRP04050. Positions 12-877, 1033-1445.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-611N.
IntActP04050. 35 interactions.
MINTMINT-432838.

Proteomic databases

PaxDbP04050.
PeptideAtlasP04050.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDL140C; YDL140C; YDL140C.
GeneID851415.
KEGGsce:YDL140C.

Organism-specific databases

CYGDYDL140c.
SGDS000002299. RPO21.

Phylogenomic databases

eggNOGCOG0086.
GeneTreeENSGT00700000105212.
HOGENOMHOG000222975.
KOK03006.
OMAKVLPWST.
OrthoDBEOG4J14H5.

Gene expression databases

ArrayExpressP04050.
GenevestigatorP04050.
GermOnlineYDL140C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D2.40.40.20. 2 hits.
InterProIPR009010. Asp_de-COase-like_dom.
IPR000722. RNA_pol_asu.
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]
PfamPF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 16 hits.
[Graphical view]
SMARTSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEPS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04050.
NextBio968606.

Entry information

Entry nameRPB1_YEAST
AccessionPrimary (citable) accession number: P04050
Secondary accession number(s): D6VRK8, Q12364, Q92315
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1997
Last modified: May 1, 2013
This is version 154 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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