Q9NYV6 (RRN3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase I-specific transcription initiation factor RRN3

Alternative name(s):
Transcription initiation factor IA
Short name=TIF-IA

Gene names

Name:	RRN3
Synonyms:	TIFIA

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	651 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for efficient transcription initiation by RNA polymerase I. Required for the formation of the competent preinitiation complex (PIC). Dissociates from pol I as a consequence of transcription. In vitro, cannot activate transcription in a subsequent transcription reaction By similarity. Ref.1 Ref.2 Ref.6 Ref.8
Subunit structure	Interacts with TWISTNB, EIF3L, TAF1B and TAF1C. Ref.6 Ref.7
Subcellular location	Nucleus › nucleolus Ref.6.
Post-translational modification	Phosphorylation is required for participation in rDNA transcription By similarity. Phosphorylated at Thr-200 by MAPK9/JNK2, which abrogates initiation complex formation. Ref.8
Sequence similarities	Belongs to the RRN3 family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell proliferation Inferred from electronic annotation. Source: Ensembl cytoplasm organization Inferred from electronic annotation. Source: Ensembl gene expression Traceable author statement. Source: Reactome homeostasis of number of cells Inferred from electronic annotation. Source: Ensembl in utero embryonic development Inferred from electronic annotation. Source: Ensembl negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator Inferred from electronic annotation. Source: Ensembl nucleolus organization Inferred from electronic annotation. Source: Ensembl positive regulation of transcription, DNA-templated Inferred from electronic annotation. Source: Ensembl regulation of DNA-templated transcription, initiation Inferred from electronic annotation. Source: Ensembl ribosome biogenesis Inferred from electronic annotation. Source: Ensembl transcription from RNA polymerase I promoter Traceable author statement. Source: Reactome transcription initiation from RNA polymerase I promoter Traceable author statement. Source: Reactome
Cellular_component	nucleolus Inferred from direct assay. Source: HPA nucleoplasm Traceable author statement. Source: Reactome nucleus Inferred from direct assay. Source: HPA
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 651	651	RNA polymerase I-specific transcription initiation factor RRN3		PRO_0000211426
Regions
	Region	500 – 651	152	Interaction with TWISTNB
	Region	557 – 651	95	Interaction with EIF3L
Amino acid modifications
	Modified residue	170	1	Phosphoserine Ref.9
	Modified residue	172	1	Phosphoserine Ref.9
	Modified residue	200	1	Phosphothreonine; by MAPK9 Ref.8
	Modified residue	640	1	Phosphoserine Ref.9 Ref.10
Natural variations
	Natural variant	348	1	I → M. Corresponds to variant rs2941256 [ dbSNP | Ensembl ].		VAR_051886
Experimental info
	Mutagenesis	411 – 415	5	Missing: Abolishes interaction with TAF1B and TAF1C. Ref.7

Sequences

	Sequence		Length	Mass (Da)
	Q9NYV6 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: C646DC6677C49895	FASTA	651	74,107
	10 20 30 40 50 60 MAAPLLHTRL PGDAAASSSA VKKLGASRTG ISNMRALEND FFNSPPRKTV RFGGTVTEVL 70 80 90 100 110 120 LKYKKGETND FELLKNQLLD PDIKDDQIIN WLLEFRSSIM YLTKDFEQLI SIILRLPWLN 130 140 150 160 170 180 RSQTVVEEYL AFLGNLVSAQ TVFLRPCLSM IASHFVPPRV IIKEGDVDVS DSDDEDDNLP 190 200 210 220 230 240 ANFDTCHRAL QIIARYVPST PWFLMPILVE KFPFVRKSER TLECYVHNLL RISVYFPTLR 250 260 270 280 290 300 HEILELIIEK LLKLDVNASR QGIEDAEETA TQTCGGTDST EGLFNMDEDE ETEHETKAGP 310 320 330 340 350 360 ERLDQMVHPV AERLDILMSL VLSYMKDVCY VDGKVDNGKT KDLYRDLINI FDKLLLPTHA 370 380 390 400 410 420 SCHVQFFMFY LCSFKLGFAE AFLEHLWKKL QDPSNPAIIR QAAGNYIGSF LARAKFIPLI 430 440 450 460 470 480 TVKSCLDLLV NWLHIYLNNQ DSGTKAFCDV ALHGPFYSAC QAVFYTFVFR HKQLLSGNLK 490 500 510 520 530 540 EGLQYLQSLN FERIVMSQLN PLKICLPSVV NFFAAITNKY QLVFCYTIIE RNNRQMLPVI 550 560 570 580 590 600 RSTAGGDSVQ ICTNPLDTFF PFDPCVLKRS KKFIDPIYQV WEDMSAEELQ EFKKPMKKDI 610 620 630 640 650 VEDEDDDFLK GEVPQNDTVI GITPSSFDTH FRSPSSSVGS PPVLYMQPSP L

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"TIF-IA, the factor mediating growth-dependent control of ribosomal RNA synthesis, is the mammalian homolog of yeast Rrn3p." Bodem J., Dobreva G., Hoffmann-Rohrer U., Iben S., Zentgraf H., Delius H., Vingron M., Grummt I. EMBO Rep. 1:171-175(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
[2]	"RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human." Moorefield B., Greene E.A., Reeder R.H. Proc. Natl. Acad. Sci. U.S.A. 97:4724-4729(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Hippocampus.
[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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Spleen.
[6]	"hRRN3 is essential in the SL1-mediated recruitment of RNA polymerase I to rRNA gene promoters." Miller G., Panov K.I., Friedrich J.K., Trinkle-Mulcahy L., Lamond A.I., Zomerdijk J.C.B.M. EMBO J. 20:1373-1382(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH TAF1B AND TAF1C.
[7]	"Multiple interactions between RNA polymerase I, TIF-IA and TAF(I) subunits regulate preinitiation complex assembly at the ribosomal gene promoter." Yuan X., Zhao J., Zentgraf H., Hoffmann-Rohrer U., Grummt I. EMBO Rep. 3:1082-1087(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TWISTNB; EIF3L; TAF1B AND TAF1C, MUTAGENESIS OF 411-LEU--LYS-415.
[8]	"The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis." Mayer C., Bierhoff H., Grummt I. Genes Dev. 19:933-941(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT THR-200 BY MAPK9/JNK2, FUNCTION.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-170; SER-172 AND SER-640, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[10]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-640, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Leukemic T-cell.
[11]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[12]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ272050 mRNA. Translation: CAC07955.1. AF227156 mRNA. Translation: AAF66160.1. AK314769 mRNA. Translation: BAG37307.1. CH471301 Genomic DNA. Translation: EAW54754.1. BC071868 mRNA. Translation: AAH71868.1. BC132688 mRNA. Translation: AAI32689.1. BC132690 mRNA. Translation: AAI32691.1.
RefSeq	NP_060897.3. NM_018427.3.
UniGene	Hs.460078.
3D structure databases
ProteinModelPortal	Q9NYV6.
SMR	Q9NYV6. Positions 54-585.
ModBase	Search...
MobiDB	Search...
Protein-protein interaction databases
BioGrid	120102. 23 interactions.
IntAct	Q9NYV6. 4 interactions.
MINT	MINT-249163.
STRING	9606.ENSP00000198767.
PTM databases
PhosphoSite	Q9NYV6.
Polymorphism databases
DMDM	74719591.
Proteomic databases
PaxDb	Q9NYV6.
PRIDE	Q9NYV6.
Protocols and materials databases
DNASU	54700.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000198767; ENSP00000198767; ENSG00000085721.
GeneID	54700.
KEGG	hsa:54700.
UCSC	uc002dde.3. human.
Organism-specific databases
CTD	54700.
GeneCards	GC16M015153.
H-InvDB	HIX0012886. HIX0038660. HIX0038739.
HGNC	HGNC:30346. RRN3.
HPA	HPA049837.
MIM	605121. gene.
neXtProt	NX_Q9NYV6.
PharmGKB	PA134878601.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG275643.
HOGENOM	HOG000236344.
HOVERGEN	HBG056994.
InParanoid	Q9NYV6.
KO	K15216.
OMA	FRWRDLT.
OrthoDB	EOG7ZGX2R.
PhylomeDB	Q9NYV6.
TreeFam	TF312979.
Enzyme and pathway databases
Reactome	REACT_1788. Transcription. REACT_71. Gene Expression.
Gene expression databases
ArrayExpress	Q9NYV6.
Bgee	Q9NYV6.
CleanEx	HS_RRN3.
Genevestigator	Q9NYV6.
Family and domain databases
InterPro	IPR007991. RNA_pol_I_trans_ini_fac_RRN3. [Graphical view]
PANTHER	PTHR12790. PTHR12790. 1 hit.
Pfam	PF05327. RRN3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
GeneWiki	RRN3.
GenomeRNAi	54700.
NextBio	57257.
PRO	Q9NYV6.
SOURCE	Search...

Entry information

Entry name

RRN3_HUMAN

Accession

Primary (citable) accession number: Q9NYV6
Secondary accession number(s): A2RTY9, Q6IPL4, Q9H4F0

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 24, 2006
Last sequence update:	October 1, 2000
Last modified:	April 16, 2014
This is version 87 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.