Q9H1D9 (RPC6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase III subunit RPC6
Short name=RNA polymerase III subunit C6

Alternative name(s):
DNA-directed RNA polymerase III subunit F
RNA polymerase III 39 kDa subunit
Short name=RPC39

Gene names

Name:

POLR3F

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	316 AA.
Sequence status	Complete.
Protein existence	Evidence 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. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway. Ref.10 Ref.11
Subunit structure	Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. RPC3/POLR3C, RPC6/POLR3F and RPC7/POLR3G form a Pol III subcomplex By similarity. Interacts with TBP and TFIIIB90 and GTF3C4. Ref.6
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the eukaryotic RPC34/RPC39 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Antiviral defense Immunity Innate immunity Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	innate immune response Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of innate immune response Inferred from mutant phenotype Ref.10. Source: UniProtKB positive regulation of interferon-beta production Inferred from mutant phenotype Ref.10. Source: UniProtKB regulation of transcription from RNA polymerase III promoter Non-traceable author statement Ref.1. Source: UniProtKB response to virus Inferred from electronic annotation. Source: UniProtKB-KW termination of RNA polymerase III transcription Traceable author statement. Source: Reactome transcription elongation from RNA polymerase III promoter Traceable author statement. Source: Reactome
Cellular component	DNA-directed RNA polymerase III complex Non-traceable author statement. Source: UniProtKB
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Non-traceable author statement Ref.1. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PNRC1	Q12796	3	EBI-710067,EBI-2827376
PRPF4B	Q13523	2	EBI-710067,EBI-395940

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 316

316

DNA-directed RNA polymerase III subunit RPC6

PRO_0000073972

Experimental info

Sequence conflict

2

1

A → G in AAB63677. Ref.1

Sequence conflict

44 – 53

10

HIEAQQRAVA → QYRSPAAGSS in AAB63677. Ref.1

Sequence conflict

255 – 290

36

AKEGT…PCGLC → CKRRHSWQCRWTHETVQGSQ SNHPSHRFGPGHPVDSA Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

316

Helix Strand Turn

Details...

Beta strand

73 – 76

4

Helix

92 – 102

11

Helix

109 – 115

7

Helix

120 – 132

13

Beta strand

135 – 139

5

Beta strand

149 – 155

7

Sequences

	Sequence		Length	Mass (Da)
	Q9H1D9 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: 49B1360AF8B365ED	FASTA	316	35,684
	10 20 30 40 50 60 MAEVKVKVQP PDADPVEIEN RIIELCHQFP HGITDQVIQN EMPHIEAQQR AVAINRLLSM 70 80 90 100 110 120 GQLDLLRSNT GLLYRIKDSQ NAGKMKGSDN QEKLVYQIIE DAGNKGIWSR DIRYKSNLPL 130 140 150 160 170 180 TEINKILKNL ESKKLIKAVK SVAASKKKVY MLYNLQPDRS VTGGAWYSDQ DFESEFVEVL 190 200 210 220 230 240 NQQCFKFLQS KAETARESKQ NPMIQRNSSF ASSHEVWKYI CELGISKVEL SMEDIETILN 250 260 270 280 290 300 TLIYDGKVEM TIIAAKEGTV GSVDGHMKLY RAVNPIIPPT GLVRAPCGLC PVFDDCHEGG 310 EISPSNCIYM TEWLEF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Three human RNA polymerase III-specific subunits form a subcomplex with a selective function in specific transcription initiation." Wang Z., Roeder R.G. Genes Dev. 11:1315-1326(1997) [PubMed: 9171375] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"The DNA sequence and comparative analysis of human chromosome 20." Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J. Nature 414:865-871(2001) [PubMed: 11780052] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain.
[6]	"The TFIIIC90 subunit of TFIIIC interacts with multiple components of the RNA polymerase III machinery and contains a histone-specific acetyltransferase activity." Hsieh Y.-J., Kundu T.K., Wang Z., Kovelman R., Roeder R.G. Mol. Cell. Biol. 19:7697-7704(1999) [PubMed: 10523658] [Abstract] Cited for: INTERACTION WITH GTF3C4.
[7]	"Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits." Hu P., Wu S., Sun Y., Yuan C.-C., Kobayashi R., Myers M.P., Hernandez N. Mol. Cell. Biol. 22:8044-8055(2002) [PubMed: 12391170] [Abstract] Cited for: IDENTIFICATION IN THE RNA POL III COMPLEX, MASS SPECTROMETRY.
[8]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]	"Solution structure of winged-helix domain in RNA polymerase III 39kDa polypeptide." RIKEN structural genomics initiative (RSGI) Submitted (OCT-2006) to the PDB data bank Cited for: STRUCTURE BY NMR OF 60-155.
[10]	"RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway." Chiu Y.-H., Macmillan J.B., Chen Z.J. Cell 138:576-591(2009) [PubMed: 19631370] [Abstract] Cited for: FUNCTION.
[11]	"RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate." Ablasser A., Bauernfeind F., Hartmann G., Latz E., Fitzgerald K.A., Hornung V. Nat. Immunol. 10:1065-1072(2009) [PubMed: 19609254] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U93869 mRNA. Translation: AAB63677.1.
AK290892 mRNA. Translation: BAF83581.1.
AL121893 Genomic DNA. Translation: CAC11110.1.
CH471133 Genomic DNA. Translation: EAX10240.1.
BC012588 mRNA. Translation: AAH12588.1.

IPI

IPI00100245.

RefSeq

NP_006457.2. NM_006466.2.

UniGene

Hs.472227.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DK5	NMR	-	A	78-155	[»]
2YU3	NMR	-	A	61-142	[»]

ProteinModelPortal

Q9H1D9.

SMR

Q9H1D9. Positions 11-155.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-34646N.

IntAct

Q9H1D9. 8 interactions.

MINT

MINT-1377146.

STRING

Q9H1D9.

PTM databases

PhosphoSite

Q9H1D9.

Polymorphism databases

DMDM

20139728.

Proteomic databases

PRIDE

Q9H1D9.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000377603; ENSP00000366828; ENSG00000132664.

GeneID

10621.

KEGG

hsa:10621.

UCSC

uc002wqv.1. human.

Organism-specific databases

CTD

10621.

GeneCards

GC20P018455.

H-InvDB

HIX0015667.

HGNC

HGNC:15763. POLR3F.

neXtProt

NX_Q9H1D9.

PharmGKB

PA33520.

GenAtlas

Search...

Phylogenomic databases

GeneTree

ENSGT00390000009679.

HOGENOM

HBG562065.

HOVERGEN

HBG006817.

InParanoid

Q9H1D9.

OMA

TPCGLCP.

OrthoDB

EOG4VQ9PP.

PhylomeDB

Q9H1D9.

Enzyme and pathway databases

Reactome

REACT_1788. Transcription.

Gene expression databases

ArrayExpress

Q9H1D9.

Bgee

Q9H1D9.

CleanEx

HS_POLR3F.

Genevestigator

Q9H1D9.

GermOnline

ENSG00000132664. Homo sapiens.

Family and domain databases

InterPro

IPR007832. RNA_pol_Rpc34.
IPR016049. RNA_pol_Rpc34-like.
IPR011991. WHTH_trsnscrt_rep_DNA-bd.
[Graphical view]

Gene3D

G3DSA:1.10.10.10. Wing_hlx_DNA_bd. 1 hit.

KO

K03025.

PANTHER

PTHR12780. RNA_pol_Rpc34. 1 hit.

Pfam

PF05158. RNA_pol_Rpc34. 1 hit.
[Graphical view]

PIRSF

PIRSF028763. RNA_pol_Rpc34. 1 hit.

ProtoNet

Search...

Other

NextBio

40356.

Entry information

Entry name

RPC6_HUMAN

Accession

Primary (citable) accession number: Q9H1D9
Secondary accession number(s): A8K4C7, O15319

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 27, 2002
Last sequence update:	March 1, 2001
Last modified:	January 25, 2012
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.