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Protein

DNA-directed RNA polymerase II subunit RPB1

Gene

RPO21

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.

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.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi67Zinc 1Combined sources2 Publications1
Metal bindingi70Zinc 1Combined sources2 Publications1
Metal bindingi77Zinc 1Combined sources2 Publications1
Metal bindingi80Zinc 1; via tele nitrogenCombined sources2 Publications1
Metal bindingi107Zinc 2Combined sources2 Publications1
Metal bindingi110Zinc 2Combined sources2 Publications1
Metal bindingi148Zinc 2Combined sources2 Publications1
Metal bindingi167Zinc 2Combined sources2 Publications1
Metal bindingi481Magnesium 1; catalyticCombined sources2 Publications1
Metal bindingi481Magnesium 2; shared with RPB2Combined sources2 Publications1
Metal bindingi483Magnesium 1; catalyticCombined sources2 Publications1
Metal bindingi483Magnesium 2; shared with RPB2Combined sources2 Publications1
Metal bindingi485Magnesium 1; catalyticCombined sources2 Publications1

GO - Molecular functioni

  • DNA binding Source: SGD
  • DNA-directed 5'-3' RNA polymerase activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • transcription, RNA-templated Source: GOC
  • transcription by RNA polymerase II Source: SGD
  • translesion synthesis Source: SGD

Keywordsi

Molecular functionDNA-binding, Nucleotidyltransferase, Transferase
Biological processTranscription
LigandMagnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-29539-MONOMER
BRENDAi2.7.7.6 984
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-6807505 RNA polymerase II transcribes snRNA genes
R-SCE-72086 mRNA Capping
R-SCE-72165 mRNA Splicing - Minor Pathway
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-SCE-9018519 Estrogen-dependent gene expression

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB1 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 1
Short name:
RNA polymerase II subunit B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
RNA polymerase II subunit B220
Gene namesi
Name:RPO21
Synonyms:RPB1, RPB220, SUA8
Ordered Locus Names:YDL140C
ORF Names:D2150
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

SGDiS000002299 RPO21

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739461 – 1733DNA-directed RNA polymerase II subunit RPB1Add BLAST1733

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki695Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki1246Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki1350Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei1471PhosphothreonineCombined sources1

Post-translational modificationi

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 heptapeptide 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 SSU72.3 Publications

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04050
PaxDbiP04050
PRIDEiP04050
TopDownProteomicsiP04050

PTM databases

CarbonylDBiP04050
iPTMnetiP04050

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Interacts with ASK10, ESS1, RTT103 and SHE2.7 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi31921, 694 interactors
ComplexPortaliCPX-2662 DNA-directed RNA polymerase II complex
DIPiDIP-611N
IntActiP04050, 56 interactors
MINTiP04050
STRINGi4932.YDL140C

Structurei

Secondary structure

11733
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP04050
SMRiP04050
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04050

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1549 – 155517
Repeati1556 – 156227
Repeati1563 – 156937
Repeati1570 – 157647
Repeati1577 – 158357
Repeati1584 – 159067
Repeati1591 – 159777
Repeati1598 – 160487
Repeati1605 – 161197
Repeati1612 – 1618107
Repeati1619 – 1625117
Repeati1626 – 1632127
Repeati1633 – 1639137
Repeati1640 – 1646147
Repeati1647 – 1653157
Repeati1654 – 1660167
Repeati1661 – 1667177
Repeati1668 – 1674187
Repeati1675 – 1681197
Repeati1682 – 1688207
Repeati1689 – 1695217
Repeati1696 – 1702227
Repeati1703 – 1709237
Repeati1710 – 171624; approximate7

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni248 – 260Lid loopAdd BLAST13
Regioni306 – 323Rudder loopAdd BLAST18
Regioni810 – 822Bridging helixAdd BLAST13
Regioni1549 – 1716C-terminal domain (CTD); 24 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[A-S-N-G]Add BLAST168

Domaini

The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.Curated

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00930000151033
HOGENOMiHOG000222975
InParanoidiP04050
KOiK03006
OMAiEDGLCGE
OrthoDBiEOG092C01XQ

Family and domain databases

Gene3Di1.10.132.30, 1 hit
3.30.1360.140, 1 hit
InterProiView protein in InterPro
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
IPR038593 RNA_pol_Rpb1_7_sf
IPR038120 Rpb1_funnel_sf
PfamiView protein in Pfam
PF04997 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, 12 hits
SMARTiView protein in SMART
SM00663 RPOLA_N, 1 hit
PROSITEiView protein in PROSITE
PS00115 RNA_POL_II_REPEAT, 22 hits

Sequencei

Sequence statusi: Complete.

P04050-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI
60 70 80 90 100
GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK
110 120 130 140 150
KVCECVCMHC GKLLLDEHNE LMRQALAIKD SKKRFAAIWT LCKTKMVCET
160 170 180 190 200
DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK LVGSWKKDRA TGDADEPELR
210 220 230 240 250
VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP VPPPPVRPSI
260 270 280 290 300
SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV
310 320 330 340 350
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR
360 370 380 390 400
TVISGDPNLE LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP
410 420 430 440 450
GAKYVIRDSG DRIDLRYSKR AGDIQLQYGW KVERHIMDND PVLFNRQPSL
460 470 480 490 500
HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA DFDGDEMNLH VPQSEETRAE
510 520 530 540 550
LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF IELDQVLNML
560 570 580 590 600
YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP
610 620 630 640 650
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ
660 670 680 690 700
KVVNFWLLHN GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN
710 720 730 740 750
LLTAKHGMTL RESFEDNVVR FLNEARDKAG RLAEVNLKDL NNVKQMVMAG
760 770 780 790 800
SKGSFINIAQ MSACVGQQSV EGKRIAFGFV DRTLPHFSKD DYSPESKGFV
810 820 830 840 850
ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV
860 870 880 890 900
HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD
910 920 930 940 950
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG
960 970 980 990 1000
EANWPLPVNI RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL
1010 1020 1030 1040 1050
RGKNEIIQNA QRDAVTLFCC LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE
1060 1070 1080 1090 1100
AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR
1110 1120 1130 1140 1150
LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH TTLKSVTIAS
1160 1170 1180 1190 1200
EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA
1210 1220 1230 1240 1250
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA
1260 1270 1280 1290 1300
ETEAEEDHML KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK
1310 1320 1330 1340 1350
EPEWVLETDG VNLSEVMTVP GIDPTRIYTN SFIDIMEVLG IEAGRAALYK
1360 1370 1380 1390 1400
EVYNVIASDG SYVNYRHMAL LVDVMTTQGG LTSVTRHGFN RSNTGALMRC
1410 1420 1430 1440 1450
SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA FDVMIDEESL
1460 1470 1480 1490 1500
VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS
1510 1520 1530 1540 1550
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS
1560 1570 1580 1590 1600
PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP
1610 1620 1630 1640 1650
TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT
1660 1670 1680 1690 1700
SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPNYSPTS
1710 1720 1730
PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR
Length:1,733
Mass (Da):191,612
Last modified:November 1, 1997 - v2
Checksum:iA45C1360FF99F968
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1514A → V in CAA26904 (PubMed:3896517).Curated1
Sequence conflicti1524G → A in CAA26904 (PubMed:3896517).Curated1
Sequence conflicti1601T → M (PubMed:3896517).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti1653 – 1659Missing in strain: A364A. 7

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
PIRiS67686 RNBY2L
RefSeqiNP_010141.1, NM_001180200.1

Genome annotation databases

EnsemblFungiiYDL140C; YDL140C; YDL140C
GeneIDi851415
KEGGisce:YDL140C

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
PIRiS67686 RNBY2L
RefSeqiNP_010141.1, NM_001180200.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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-B1675-1688[»]
2LO6NMR-B1675-1688[»]
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[»]
3J0Kelectron microscopy36.00A1-1455[»]
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[»]
4BXXX-ray3.28A1-1733[»]
4BXZX-ray4.80A1-1733[»]
4BY1X-ray3.60A1-1733[»]
4BY7X-ray3.15A1-1733[»]
4GWQX-ray4.50H1619-1653[»]
4V1Melectron microscopy6.60A1-1733[»]
4V1Nelectron microscopy7.80A1-1733[»]
4V1Oelectron microscopy9.70A1-1733[»]
4X67X-ray4.10A1-1733[»]
4X6AX-ray3.96A1-1733[»]
4Y52X-ray3.50A1-1733[»]
4Y7NX-ray3.30A1-1733[»]
5C3EX-ray3.70A1-1733[»]
5C44X-ray3.95A1-1733[»]
5C4AX-ray4.20A1-1733[»]
5C4JX-ray4.00A1-1733[»]
5C4XX-ray4.00A1-1733[»]
5FMFelectron microscopy6.00A1-1733[»]
5FYWelectron microscopy4.35A1-1733[»]
5FZ5electron microscopy8.80A1-1733[»]
5IP7X-ray3.52A2-1733[»]
5IP9X-ray3.90A2-1733[»]
5LVFNMR-B1673-1688[»]
5M9DNMR-B1678-1693[»]
5OQJelectron microscopy4.70A1-1733[»]
5OQMelectron microscopy5.80A1-1733[»]
5OT2X-ray3.20A1-1733[»]
5SVAelectron microscopy15.30A1-1733[»]
k1666-1690[»]
5U5QX-ray3.80A1-1733[»]
5VKLX-ray2.20B1476-1498[»]
5VKOX-ray1.80B1468-1500[»]
5VVRelectron microscopy5.80A1-1733[»]
5VVSelectron microscopy6.40A1-1733[»]
5W4UX-ray3.60A1-1733[»]
5W51X-ray3.40A1-1733[»]
6BLOX-ray3.40A1-1733[»]
6BLPX-ray3.20A1-1733[»]
6BM2X-ray3.40A1-1733[»]
6BM4X-ray2.95A1-1733[»]
6BQFX-ray3.35A1-1733[»]
ProteinModelPortaliP04050
SMRiP04050
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31921, 694 interactors
ComplexPortaliCPX-2662 DNA-directed RNA polymerase II complex
DIPiDIP-611N
IntActiP04050, 56 interactors
MINTiP04050
STRINGi4932.YDL140C

PTM databases

CarbonylDBiP04050
iPTMnetiP04050

Proteomic databases

MaxQBiP04050
PaxDbiP04050
PRIDEiP04050
TopDownProteomicsiP04050

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL140C; YDL140C; YDL140C
GeneIDi851415
KEGGisce:YDL140C

Organism-specific databases

SGDiS000002299 RPO21

Phylogenomic databases

GeneTreeiENSGT00930000151033
HOGENOMiHOG000222975
InParanoidiP04050
KOiK03006
OMAiEDGLCGE
OrthoDBiEOG092C01XQ

Enzyme and pathway databases

BioCyciYEAST:G3O-29539-MONOMER
BRENDAi2.7.7.6 984
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-6807505 RNA polymerase II transcribes snRNA genes
R-SCE-72086 mRNA Capping
R-SCE-72165 mRNA Splicing - Minor Pathway
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-SCE-9018519 Estrogen-dependent gene expression

Miscellaneous databases

EvolutionaryTraceiP04050
PROiPR:P04050

Family and domain databases

Gene3Di1.10.132.30, 1 hit
3.30.1360.140, 1 hit
InterProiView protein in InterPro
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
IPR038593 RNA_pol_Rpb1_7_sf
IPR038120 Rpb1_funnel_sf
PfamiView protein in Pfam
PF04997 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, 12 hits
SMARTiView protein in SMART
SM00663 RPOLA_N, 1 hit
PROSITEiView protein in PROSITE
PS00115 RNA_POL_II_REPEAT, 22 hits
ProtoNetiSearch...

Entry informationi

Entry nameiRPB1_YEAST
AccessioniPrimary (citable) accession number: P04050
Secondary accession number(s): D6VRK8, Q12364, Q92315
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1997
Last modified: November 7, 2018
This is version 214 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names
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