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Protein

DNA-directed RNA polymerase II subunit RPB4

Gene

POLR2D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity).By similarity1 Publication

GO - Molecular functioni

  • DNA-directed RNA polymerase activity Source: UniProtKB
  • nucleotide binding Source: InterPro
  • translation initiation factor binding Source: GO_Central

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription

Enzyme and pathway databases

ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-113418. Formation of the Early Elongation Complex.
R-HSA-167152. Formation of HIV elongation complex in the absence of HIV Tat.
R-HSA-167158. Formation of the HIV-1 Early Elongation Complex.
R-HSA-167160. RNA Pol II CTD phosphorylation and interaction with CE.
R-HSA-167161. HIV Transcription Initiation.
R-HSA-167162. RNA Polymerase II HIV Promoter Escape.
R-HSA-167172. Transcription of the HIV genome.
R-HSA-167200. Formation of HIV-1 elongation complex containing HIV-1 Tat.
R-HSA-167238. Pausing and recovery of Tat-mediated HIV elongation.
R-HSA-167242. Abortive elongation of HIV-1 transcript in the absence of Tat.
R-HSA-167243. Tat-mediated HIV elongation arrest and recovery.
R-HSA-167246. Tat-mediated elongation of the HIV-1 transcript.
R-HSA-167287. HIV elongation arrest and recovery.
R-HSA-167290. Pausing and recovery of HIV elongation.
R-HSA-168325. Viral Messenger RNA Synthesis.
R-HSA-203927. MicroRNA (miRNA) biogenesis.
R-HSA-452723. Transcriptional regulation of pluripotent stem cells.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5601884. PIWI-interacting RNA (piRNA) biogenesis.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-72086. mRNA Capping.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-HSA-73776. RNA Polymerase II Promoter Escape.
R-HSA-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-HSA-75953. RNA Polymerase II Transcription Initiation.
R-HSA-75955. RNA Polymerase II Transcription Elongation.
R-HSA-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-HSA-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB4
Short name:
RNA polymerase II subunit B4
Alternative name(s):
DNA-directed RNA polymerase II subunit D
RNA polymerase II 16 kDa subunit
Short name:
RPB16
Gene namesi
Name:POLR2D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:9191. POLR2D.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: GO_Central
  • DNA-directed RNA polymerase II, core complex Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33511.

Polymorphism and mutation databases

BioMutaiPOLR2D.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 142142DNA-directed RNA polymerase II subunit RPB4PRO_0000073981Add
BLAST

Proteomic databases

EPDiO15514.
MaxQBiO15514.
PaxDbiO15514.
PeptideAtlasiO15514.
PRIDEiO15514.

PTM databases

iPTMnetiO15514.
PhosphoSiteiO15514.

Expressioni

Gene expression databases

BgeeiO15514.
CleanExiHS_POLR2D.
ExpressionAtlasiO15514. baseline and differential.
GenevisibleiO15514. HS.

Organism-specific databases

HPAiHPA046092.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111429. 64 interactions.
DIPiDIP-32912N.
IntActiO15514. 13 interactions.
STRINGi9606.ENSP00000272645.

Structurei

Secondary structure

1
142
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi17 – 193Combined sources
Beta strandi24 – 285Combined sources
Helixi34 – 4916Combined sources
Helixi59 – 7012Combined sources
Helixi77 – 8812Combined sources
Helixi94 – 10310Combined sources
Helixi108 – 1147Combined sources
Helixi116 – 1183Combined sources
Turni119 – 1213Combined sources
Helixi124 – 13714Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C35X-ray2.70A/C/E/G1-142[»]
ProteinModelPortaliO15514.
SMRiO15514. Positions 14-141.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO15514.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2351. Eukaryota.
COG5250. LUCA.
GeneTreeiENSGT00390000004912.
HOGENOMiHOG000195281.
HOVERGENiHBG002800.
InParanoidiO15514.
KOiK03012.
OMAiEDAAECK.
OrthoDBiEOG7RFTK1.
PhylomeDBiO15514.
TreeFamiTF103039.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.

Sequencei

Sequence statusi: Complete.

O15514-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES
60 70 80 90 100
AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL
110 120 130 140
ANLCPETAEE SKALIPSLEG RFEDEELQQI LDDIQTKRSF QY
Length:142
Mass (Da):16,311
Last modified:January 1, 1998 - v1
Checksum:i8A670386C433BE93
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89387 Genomic DNA. Translation: AAC52056.1.
U85510 mRNA. Translation: AAC80226.1.
BC017205 mRNA. Translation: AAH17205.1.
BC093795 mRNA. Translation: AAH93795.1.
BC093797 mRNA. Translation: AAH93797.1.
CCDSiCCDS2151.1.
RefSeqiNP_004796.1. NM_004805.3.
UniGeneiHs.715348.

Genome annotation databases

EnsembliENST00000272645; ENSP00000272645; ENSG00000144231.
GeneIDi5433.
KEGGihsa:5433.
UCSCiuc002tpj.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89387 Genomic DNA. Translation: AAC52056.1.
U85510 mRNA. Translation: AAC80226.1.
BC017205 mRNA. Translation: AAH17205.1.
BC093795 mRNA. Translation: AAH93795.1.
BC093797 mRNA. Translation: AAH93797.1.
CCDSiCCDS2151.1.
RefSeqiNP_004796.1. NM_004805.3.
UniGeneiHs.715348.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C35X-ray2.70A/C/E/G1-142[»]
ProteinModelPortaliO15514.
SMRiO15514. Positions 14-141.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111429. 64 interactions.
DIPiDIP-32912N.
IntActiO15514. 13 interactions.
STRINGi9606.ENSP00000272645.

PTM databases

iPTMnetiO15514.
PhosphoSiteiO15514.

Polymorphism and mutation databases

BioMutaiPOLR2D.

Proteomic databases

EPDiO15514.
MaxQBiO15514.
PaxDbiO15514.
PeptideAtlasiO15514.
PRIDEiO15514.

Protocols and materials databases

DNASUi5433.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000272645; ENSP00000272645; ENSG00000144231.
GeneIDi5433.
KEGGihsa:5433.
UCSCiuc002tpj.4. human.

Organism-specific databases

CTDi5433.
GeneCardsiPOLR2D.
HGNCiHGNC:9191. POLR2D.
HPAiHPA046092.
MIMi606017. gene.
neXtProtiNX_O15514.
PharmGKBiPA33511.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2351. Eukaryota.
COG5250. LUCA.
GeneTreeiENSGT00390000004912.
HOGENOMiHOG000195281.
HOVERGENiHBG002800.
InParanoidiO15514.
KOiK03012.
OMAiEDAAECK.
OrthoDBiEOG7RFTK1.
PhylomeDBiO15514.
TreeFamiTF103039.

Enzyme and pathway databases

ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-113418. Formation of the Early Elongation Complex.
R-HSA-167152. Formation of HIV elongation complex in the absence of HIV Tat.
R-HSA-167158. Formation of the HIV-1 Early Elongation Complex.
R-HSA-167160. RNA Pol II CTD phosphorylation and interaction with CE.
R-HSA-167161. HIV Transcription Initiation.
R-HSA-167162. RNA Polymerase II HIV Promoter Escape.
R-HSA-167172. Transcription of the HIV genome.
R-HSA-167200. Formation of HIV-1 elongation complex containing HIV-1 Tat.
R-HSA-167238. Pausing and recovery of Tat-mediated HIV elongation.
R-HSA-167242. Abortive elongation of HIV-1 transcript in the absence of Tat.
R-HSA-167243. Tat-mediated HIV elongation arrest and recovery.
R-HSA-167246. Tat-mediated elongation of the HIV-1 transcript.
R-HSA-167287. HIV elongation arrest and recovery.
R-HSA-167290. Pausing and recovery of HIV elongation.
R-HSA-168325. Viral Messenger RNA Synthesis.
R-HSA-203927. MicroRNA (miRNA) biogenesis.
R-HSA-452723. Transcriptional regulation of pluripotent stem cells.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5601884. PIWI-interacting RNA (piRNA) biogenesis.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-72086. mRNA Capping.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-HSA-73776. RNA Polymerase II Promoter Escape.
R-HSA-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-HSA-75953. RNA Polymerase II Transcription Initiation.
R-HSA-75955. RNA Polymerase II Transcription Elongation.
R-HSA-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-HSA-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

ChiTaRSiPOLR2D. human.
EvolutionaryTraceiO15514.
GeneWikiiRNA_polymerase_II_subunit_B4.
GenomeRNAii5433.
NextBioi21021.
PROiO15514.
SOURCEiSearch...

Gene expression databases

BgeeiO15514.
CleanExiHS_POLR2D.
ExpressionAtlasiO15514. baseline and differential.
GenevisibleiO15514. HS.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II."
    Khazak V., Estojak J., Cho H., Majors J.A., Sonoda G., Testa J.R., Golemis E.A.
    Mol. Cell. Biol. 18:1935-1945(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
    Tissue: Cervix carcinoma.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lung and Skin.
  3. "Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes."
    Kershnar E., Wu S.-Y., Chiang C.-M.
    J. Biol. Chem. 273:34444-34453(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II CORE-COMPLEX, SUBCELLULAR LOCATION.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. "Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II."
    Meka H., Werner F., Cordell S.C., Onesti S., Brick P.
    Nucleic Acids Res. 33:6435-6444(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF THE POL II RPB4-RPB7 SUBCOMPLEX.

Entry informationi

Entry nameiRPB4_HUMAN
AccessioniPrimary (citable) accession number: O15514
Secondary accession number(s): Q52LT4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 1, 1998
Last modified: April 13, 2016
This is version 154 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.