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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:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>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

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>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

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-29539-MONOMER

BRENDA Comprehensive Enzyme Information System

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BRENDAi
2.7.7.6 984

Reactome - a knowledgebase of biological pathways and processes

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Reactomei
R-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

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:RPO21
Synonyms:RPB1, RPB220, SUA8
Ordered Locus Names:YDL140C
ORF Names:D2150
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome IV

Organism-specific databases

Saccharomyces Genome Database

More...
SGDi
S000002299 RPO21

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000739461 – 1733DNA-directed RNA polymerase II subunit RPB1Add BLAST1733

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>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
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei1471PhosphothreonineCombined sources1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>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

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P04050

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
P04050

PRoteomics IDEntifications database

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PRIDEi
P04050

Consortium for Top Down Proteomics

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TopDownProteomicsi
P04050

PTM databases

CarbonylDB database of protein carbonylation sites

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CarbonylDBi
P04050

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
P04050

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

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

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
31921, 694 interactors

ComplexPortal: manually curated resource of macromolecular complexes

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ComplexPortali
CPX-2662 DNA-directed RNA polymerase II complex

Database of interacting proteins

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DIPi
DIP-611N

Protein interaction database and analysis system

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IntActi
P04050, 56 interactors

Molecular INTeraction database

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MINTi
P04050

STRING: functional protein association networks

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STRINGi
4932.YDL140C

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

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

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P04050

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P04050

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

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EvolutionaryTracei
P04050

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>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
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>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

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

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

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

Ensembl GeneTree

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GeneTreei
ENSGT00930000151033

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000222975

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P04050

KEGG Orthology (KO)

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KOi
K03006

Identification of Orthologs from Complete Genome Data

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OMAi
EDGLCGE

Database of Orthologous Groups

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OrthoDBi
EOG092C01XQ

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.10.132.30, 1 hit
3.30.1360.140, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View 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

Pfam protein domain database

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Pfami
View 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

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00663 RPOLA_N, 1 hit

PROSITE; a protein domain and family database

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PROSITEi
View protein in PROSITE
PS00115 RNA_POL_II_REPEAT, 22 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iA45C1360FF99F968
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>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
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti1653 – 1659Missing in strain: A364A. 7

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
S67686 RNBY2L

NCBI Reference Sequences

More...
RefSeqi
NP_010141.1, NM_001180200.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YDL140C_mRNA; YDL140C_mRNA; YDL140C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
851415

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YDL140C

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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_mRNA; YDL140C_mRNA; 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

Protein Ontology

More...
PROi
PR: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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRPB1_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P04050
Secondary accession number(s): D6VRK8, Q12364, Q92315
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1997
Last modified: December 5, 2018
This is version 215 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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