RPB4_HUMAN
ID RPB4_HUMAN Reviewed; 142 AA.
AC O15514; Q52LT4;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=DNA-directed RNA polymerase II subunit RPB4;
DE Short=RNA polymerase II subunit B4;
DE AltName: Full=DNA-directed RNA polymerase II subunit D;
DE AltName: Full=RNA polymerase II 16 kDa subunit;
DE Short=RPB16;
GN Name=POLR2D;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RC TISSUE=Cervix carcinoma;
RX PubMed=9528765; DOI=10.1128/mcb.18.4.1935;
RA Khazak V., Estojak J., Cho H., Majors J.A., Sonoda G., Testa J.R.,
RA Golemis E.A.;
RT "Analysis of the interaction of the novel RNA polymerase II (pol II)
RT subunit hsRPB4 with its partner hsRPB7 and with pol II.";
RL Mol. Cell. Biol. 18:1935-1945(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung, and Skin;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II CORE-COMPLEX, AND
RP SUBCELLULAR LOCATION.
RX PubMed=9852112; DOI=10.1074/jbc.273.51.34444;
RA Kershnar E., Wu S.-Y., Chiang C.-M.;
RT "Immunoaffinity purification and functional characterization of human
RT transcription factor IIH and RNA polymerase II from clonal cell lines that
RT conditionally express epitope-tagged subunits of the multiprotein
RT complexes.";
RL J. Biol. Chem. 273:34444-34453(1998).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF THE POL II RPB4-RPB7 SUBCOMPLEX.
RX PubMed=16282592; DOI=10.1093/nar/gki945;
RA Meka H., Werner F., Cordell S.C., Onesti S., Brick P.;
RT "Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA
RT polymerase II.";
RL Nucleic Acids Res. 33:6435-6444(2005).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Component of RNA polymerase II which synthesizes mRNA precursors and
CC many functional non-coding RNAs. Pol II is the central component of the
CC basal RNA polymerase II transcription machinery. It is composed of
CC mobile elements that move relative to each other. RPB4 is part of a
CC subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and
CC RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems
CC to lock the clamp via RPB7 in the closed conformation thus preventing
CC double-stranded DNA to enter the active site cleft. The RPB4-RPB7
CC subcomplex binds single-stranded DNA and RNA (By similarity).
CC {ECO:0000250, ECO:0000269|PubMed:9852112}.
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the
CC 10-subunit Pol II core complex. {ECO:0000269|PubMed:9852112}.
CC -!- INTERACTION:
CC O15514; P62875: POLR2L; NbExp=3; IntAct=EBI-394737, EBI-359527;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9852112}.
CC -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC family. {ECO:0000305}.
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DR EMBL; U89387; AAC52056.1; -; Genomic_DNA.
DR EMBL; U85510; AAC80226.1; -; mRNA.
DR EMBL; BC017205; AAH17205.1; -; mRNA.
DR EMBL; BC093795; AAH93795.1; -; mRNA.
DR EMBL; BC093797; AAH93797.1; -; mRNA.
DR CCDS; CCDS2151.1; -.
DR RefSeq; NP_004796.1; NM_004805.3.
DR PDB; 2C35; X-ray; 2.70 A; A/C/E/G=1-142.
DR PDB; 5IY6; EM; 7.20 A; D=1-142.
DR PDB; 5IY7; EM; 8.60 A; D=1-142.
DR PDB; 5IY8; EM; 7.90 A; D=1-142.
DR PDB; 5IY9; EM; 6.30 A; D=1-142.
DR PDB; 5IYA; EM; 5.40 A; D=1-142.
DR PDB; 5IYB; EM; 3.90 A; D=1-142.
DR PDB; 5IYC; EM; 3.90 A; D=1-142.
DR PDB; 5IYD; EM; 3.90 A; D=1-142.
DR PDB; 6DRD; EM; 3.90 A; D=1-142.
DR PDB; 6O9L; EM; 7.20 A; D=1-142.
DR PDB; 6XRE; EM; 4.60 A; D=1-142.
DR PDB; 7LBM; EM; 4.80 A; D=1-142.
DR PDBsum; 2C35; -.
DR PDBsum; 5IY6; -.
DR PDBsum; 5IY7; -.
DR PDBsum; 5IY8; -.
DR PDBsum; 5IY9; -.
DR PDBsum; 5IYA; -.
DR PDBsum; 5IYB; -.
DR PDBsum; 5IYC; -.
DR PDBsum; 5IYD; -.
DR PDBsum; 6DRD; -.
DR PDBsum; 6O9L; -.
DR PDBsum; 6XRE; -.
DR PDBsum; 7LBM; -.
DR AlphaFoldDB; O15514; -.
DR SMR; O15514; -.
DR BioGRID; 111429; 126.
DR CORUM; O15514; -.
DR DIP; DIP-32912N; -.
DR IntAct; O15514; 64.
DR MINT; O15514; -.
DR STRING; 9606.ENSP00000272645; -.
DR iPTMnet; O15514; -.
DR PhosphoSitePlus; O15514; -.
DR BioMuta; POLR2D; -.
DR EPD; O15514; -.
DR jPOST; O15514; -.
DR MassIVE; O15514; -.
DR MaxQB; O15514; -.
DR PaxDb; O15514; -.
DR PeptideAtlas; O15514; -.
DR PRIDE; O15514; -.
DR ProteomicsDB; 48705; -.
DR Antibodypedia; 33469; 194 antibodies from 28 providers.
DR DNASU; 5433; -.
DR Ensembl; ENST00000272645.9; ENSP00000272645.3; ENSG00000144231.11.
DR GeneID; 5433; -.
DR KEGG; hsa:5433; -.
DR MANE-Select; ENST00000272645.9; ENSP00000272645.3; NM_004805.4; NP_004796.1.
DR UCSC; uc002tpj.4; human.
DR CTD; 5433; -.
DR DisGeNET; 5433; -.
DR GeneCards; POLR2D; -.
DR HGNC; HGNC:9191; POLR2D.
DR HPA; ENSG00000144231; Tissue enhanced (testis).
DR MIM; 606017; gene.
DR neXtProt; NX_O15514; -.
DR OpenTargets; ENSG00000144231; -.
DR PharmGKB; PA33511; -.
DR VEuPathDB; HostDB:ENSG00000144231; -.
DR eggNOG; KOG2351; Eukaryota.
DR GeneTree; ENSGT00390000004912; -.
DR InParanoid; O15514; -.
DR OMA; AQLGTLC; -.
DR OrthoDB; 1480091at2759; -.
DR PhylomeDB; O15514; -.
DR TreeFam; TF103039; -.
DR PathwayCommons; O15514; -.
DR Reactome; R-HSA-112382; Formation of RNA Pol II elongation complex.
DR Reactome; R-HSA-113418; Formation of the Early Elongation Complex.
DR Reactome; R-HSA-167152; Formation of HIV elongation complex in the absence of HIV Tat.
DR Reactome; R-HSA-167158; Formation of the HIV-1 Early Elongation Complex.
DR Reactome; R-HSA-167160; RNA Pol II CTD phosphorylation and interaction with CE during HIV infection.
DR Reactome; R-HSA-167161; HIV Transcription Initiation.
DR Reactome; R-HSA-167162; RNA Polymerase II HIV Promoter Escape.
DR Reactome; R-HSA-167172; Transcription of the HIV genome.
DR Reactome; R-HSA-167200; Formation of HIV-1 elongation complex containing HIV-1 Tat.
DR Reactome; R-HSA-167238; Pausing and recovery of Tat-mediated HIV elongation.
DR Reactome; R-HSA-167242; Abortive elongation of HIV-1 transcript in the absence of Tat.
DR Reactome; R-HSA-167243; Tat-mediated HIV elongation arrest and recovery.
DR Reactome; R-HSA-167246; Tat-mediated elongation of the HIV-1 transcript.
DR Reactome; R-HSA-167287; HIV elongation arrest and recovery.
DR Reactome; R-HSA-167290; Pausing and recovery of HIV elongation.
DR Reactome; R-HSA-168325; Viral Messenger RNA Synthesis.
DR Reactome; R-HSA-203927; MicroRNA (miRNA) biogenesis.
DR Reactome; R-HSA-5578749; Transcriptional regulation by small RNAs.
DR Reactome; R-HSA-5601884; PIWI-interacting RNA (piRNA) biogenesis.
DR Reactome; R-HSA-5617472; Activation of anterior HOX genes in hindbrain development during early embryogenesis.
DR Reactome; R-HSA-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-HSA-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-HSA-6781827; Transcription-Coupled Nucleotide Excision Repair (TC-NER).
DR Reactome; R-HSA-6782135; Dual incision in TC-NER.
DR Reactome; R-HSA-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-HSA-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-HSA-6803529; FGFR2 alternative splicing.
DR Reactome; R-HSA-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-HSA-72086; mRNA Capping.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-HSA-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-HSA-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR Reactome; R-HSA-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-HSA-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-HSA-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-HSA-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-HSA-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-HSA-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-HSA-8851708; Signaling by FGFR2 IIIa TM.
DR Reactome; R-HSA-9018519; Estrogen-dependent gene expression.
DR Reactome; R-HSA-9670095; Inhibition of DNA recombination at telomere.
DR SignaLink; O15514; -.
DR SIGNOR; O15514; -.
DR BioGRID-ORCS; 5433; 808 hits in 1096 CRISPR screens.
DR ChiTaRS; POLR2D; human.
DR EvolutionaryTrace; O15514; -.
DR GeneWiki; RNA_polymerase_II_subunit_B4; -.
DR GenomeRNAi; 5433; -.
DR Pharos; O15514; Tdark.
DR PRO; PR:O15514; -.
DR Proteomes; UP000005640; Chromosome 2.
DR RNAct; O15514; protein.
DR Bgee; ENSG00000144231; Expressed in endothelial cell and 183 other tissues.
DR ExpressionAtlas; O15514; baseline and differential.
DR Genevisible; O15514; HS.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0016607; C:nuclear speck; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0031369; F:translation initiation factor binding; IBA:GO_Central.
DR GO; GO:0031990; P:mRNA export from nucleus in response to heat stress; IBA:GO_Central.
DR GO; GO:0000288; P:nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IBA:GO_Central.
DR GO; GO:0045948; P:positive regulation of translational initiation; IBA:GO_Central.
DR GO; GO:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IBA:GO_Central.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IDA:UniProtKB.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR Gene3D; 1.20.1250.40; -; 1.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR InterPro; IPR045222; Rpb4-like.
DR InterPro; IPR005574; Rpb4/RPC9.
DR InterPro; IPR038324; Rpb4/RPC9_sf.
DR PANTHER; PTHR21297; PTHR21297; 1.
DR Pfam; PF03874; RNA_pol_Rpb4; 1.
DR SMART; SM00657; RPOL4c; 1.
DR SUPFAM; SSF47819; SSF47819; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-directed RNA polymerase; Nucleus; Reference proteome;
KW Transcription.
FT CHAIN 1..142
FT /note="DNA-directed RNA polymerase II subunit RPB4"
FT /id="PRO_0000073981"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:2C35"
FT STRAND 24..28
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 34..49
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 59..70
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 77..88
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 108..114
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:2C35"
FT TURN 119..121
FT /evidence="ECO:0007829|PDB:2C35"
FT HELIX 124..137
FT /evidence="ECO:0007829|PDB:2C35"
SQ SEQUENCE 142 AA; 16311 MW; 8A670386C433BE93 CRC64;
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV
FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL ANLCPETAEE SKALIPSLEG
RFEDEELQQI LDDIQTKRSF QY
