Q9H1D9 · RPC6_HUMAN
- ProteinDNA-directed RNA polymerase III subunit RPC6
- GenePOLR3F
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids316 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (PubMed:20413673, PubMed:21358628, PubMed:33558764, PubMed:34675218).
Specific peripheric component of RNA polymerase III (Pol III) which synthesizes small non-coding RNAs including 5S rRNA, snRNAs, tRNAs and miRNAs from at least 500 distinct genomic loci. Part of POLR3C/RPC3-POLR3F/RPC6-POLR3G/RPC7 heterotrimer that coordinates the dynamics of Pol III stalk and clamp modules during the transition from apo to elongation state (PubMed:20413673, PubMed:33558764, PubMed:33558766).
Pol III plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses, including varicella zoster virus. Acts as a nuclear and cytosolic DNA sensor detecting AT-rich DNA, 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 (PubMed:19609254, PubMed:19631370, PubMed:30211253).
Preferentially binds double-stranded DNA (dsDNA) (PubMed:21358628).
Specific peripheric component of RNA polymerase III (Pol III) which synthesizes small non-coding RNAs including 5S rRNA, snRNAs, tRNAs and miRNAs from at least 500 distinct genomic loci. Part of POLR3C/RPC3-POLR3F/RPC6-POLR3G/RPC7 heterotrimer that coordinates the dynamics of Pol III stalk and clamp modules during the transition from apo to elongation state (PubMed:20413673, PubMed:33558764, PubMed:33558766).
Pol III plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses, including varicella zoster virus. Acts as a nuclear and cytosolic DNA sensor detecting AT-rich DNA, 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 (PubMed:19609254, PubMed:19631370, PubMed:30211253).
Preferentially binds double-stranded DNA (dsDNA) (PubMed:21358628).
Features
Showing features for binding site.
GO annotations
all annotations | all molecular function | virus receptor activity | dna binding | rna binding | cytoskeletal motor activity | catalytic activity | gtpase activity | structural molecule activity | transporter activity | cytoskeletal protein binding | lipid binding | cyclase activity | antioxidant activity | oxidoreductase activity | transferase activity | hydrolase activity | lyase activity | isomerase activity | ligase activity | protein tag activity | cargo receptor activity | histone binding | protein folding chaperone | translation regulator activity | nutrient reservoir activity | receptor ligand activity | molecular transducer activity | molecular adaptor activity | toxin activity | cell adhesion mediator activity | molecular function regulator activity | virus coreceptor activity | catalytic activity, acting on a protein | catalytic activity, acting on dna | catalytic activity, acting on rna | molecular carrier activity | transcription regulator activity | general transcription initiation factor activity | molecular sensor activity | molecular sequestering activity | atp-dependent activity | other molecular function | all biological process | mitotic cell cycle | cytokinesis | cytoplasmic translation | immune system process | muscle system process | circulatory system process | renal system process | respiratory system process | carbohydrate metabolic process | generation of precursor metabolites and energy | dna replication | dna repair | dna recombination | chromatin organization | dna-templated transcription | regulation of dna-templated transcription | trna metabolic process | protein folding | protein glycosylation | amino acid metabolic process | modified amino acid metabolic process | lipid metabolic process | vitamin metabolic process | sulfur compound metabolic process | intracellular protein transport | nucleocytoplasmic transport | autophagy | inflammatory response | mitochondrion organization | cytoskeleton organization | microtubule-based movement | peroxisome organization | lysosome organization | chromosome segregation | cell adhesion | establishment or maintenance of cell polarity | programmed cell death | photosynthesis | mrna metabolic process | snrna metabolic process | vesicle-mediated transport | reproductive process | digestive system process | signaling | cell differentiation | protein catabolic process | extracellular matrix organization | regulatory ncrna-mediated gene silencing | telomere organization | cell junction organization | wound healing | ribosome biogenesis | cilium organization | anatomical structure development | cell motility | nervous system process | endocrine process | protein maturation | transmembrane transport | nucleobase-containing small molecule metabolic process | hepaticobiliary system process | membrane organization | protein-containing complex assembly | cell wall organization or biogenesis | nitrogen cycle metabolic process | protein localization to plasma membrane | defense response to other organism | detoxification | meiotic nuclear division | mitotic nuclear division | mitochondrial gene expression | carbohydrate derivative metabolic process | other biological process | all cellular component | nuclear chromosome | extracellular region | extracellular space | cell wall | nucleus | nuclear envelope | nucleoplasm | chromosome | nucleolus | mitochondrion | lysosome | endosome | vacuole | peroxisome | endoplasmic reticulum | golgi apparatus | lipid droplet | microtubule organizing center | cytosol | ribosome | cytoskeleton | plasma membrane | cilium | plastid | thylakoid | external encapsulating structure | extracellular matrix | cytoplasmic vesicle | organelle | other cellular component | |||
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Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Cellular Component | nucleoplasm | |
Cellular Component | RNA polymerase III complex | |
Molecular Function | 4 iron, 4 sulfur cluster binding | |
Molecular Function | DNA-directed 5'-3' RNA polymerase activity | |
Molecular Function | double-stranded DNA binding | |
Biological Process | defense response to virus | |
Biological Process | innate immune response | |
Biological Process | positive regulation of innate immune response | |
Biological Process | positive regulation of interferon-beta production | |
Biological Process | regulation of transcription by RNA polymerase III | |
Biological Process | transcription by RNA polymerase III |
Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA-directed RNA polymerase III subunit RPC6
- Short namesRNA polymerase III subunit C6
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ9H1D9
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Disease & Variants
Involvement in disease
Immunodeficiency 101, varicella zoster virus-specific (IMD101)
- Note
- DescriptionAn autosomal dominant immunologic disorder characterized by reactivation of varicella zoster virus (VZV) infection in adulthood after primary childhood infection with VZV. The viral reactivation manifests as central nervous system vasculitis with stroke-like episodes and lacunar infarcts on brain imaging. Features include headache, hemiparesis, impaired balance, and other neurologic signs.
- See alsoMIM:619872
Natural variants in IMD101
Variant ID | Position(s) | Change | Description | |
---|---|---|---|---|
VAR_087291 | 50 | R>W | in IMD101; uncertain significance; dbSNP:rs756434857 |
Features
Showing features for natural variant, mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Natural variant | VAR_087291 | 50 | in IMD101; uncertain significance; dbSNP:rs756434857 | |||
Sequence: R → W | ||||||
Mutagenesis | 137-140 | Strongly impaired dsDNA-binding. No effect on interaction with POLR3C. | ||||
Sequence: KAVK → EAVE | ||||||
Mutagenesis | 173-175 | Strongly impaired dsDNA-binding. No effect on interaction with POLR3C. | ||||
Sequence: ESE → KSK |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 286 variants from UniProt as well as other sources including ClinVar and dbSNP.
Organism-specific databases
Miscellaneous
Genetic variation databases
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain, cross-link.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Modified residue | 2 | N-acetylalanine | ||||
Sequence: A | ||||||
Chain | PRO_0000073972 | 2-316 | DNA-directed RNA polymerase III subunit RPC6 | |||
Sequence: AEVKVKVQPPDADPVEIENRIIELCHQFPHGITDQVIQNEMPHIEAQQRAVAINRLLSMGQLDLLRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPIIPPTGLVRAPCGLCPVFDDCHEGGEISPSNCIYMTEWLEF | ||||||
Cross-link | 5 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Cross-link | 7 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K |
Keywords
- PTM
Proteomic databases
PTM databases
Interaction
Subunit
Component of the RNA polymerase III complex consisting of 17 subunits: a ten-subunit horseshoe-shaped catalytic core composed of POLR3A/RPC1, POLR3B/RPC2, POLR1C/RPAC1, POLR1D/RPAC2, POLR3K/RPC10, POLR2E/RPABC1, POLR2F/RPABC2, POLR2H/RPABC3, POLR2K/RPABC4 and POLR2L/RPABC5; a mobile stalk composed of two subunits POLR3H/RPC8 and CRCP/RPC9, protruding from the core and functioning primarily in transcription initiation; and additional subunits homologous to general transcription factors of the RNA polymerase II machinery, POLR3C/RPC3-POLR3F/RPC6-POLR3G/RPC7 heterotrimer required for transcription initiation and POLR3D/RPC4-POLR3E/RPC5 heterodimer involved in both transcription initiation and termination (PubMed:12391170, PubMed:33335104, PubMed:33558764, PubMed:33558766, PubMed:33674783, PubMed:34675218).
Directly interacts with POLR3C (PubMed:21358628).
Interacts with TBP and TFIIIB90 and GTF3C4 (By similarity) (PubMed:10523658).
Interacts with MAF1 (PubMed:18377933).
As part of the RNA polymerase III complex, interacts with PKP2 (PubMed:11416169).
Directly interacts with POLR3C (PubMed:21358628).
Interacts with TBP and TFIIIB90 and GTF3C4 (By similarity) (PubMed:10523658).
Interacts with MAF1 (PubMed:18377933).
As part of the RNA polymerase III complex, interacts with PKP2 (PubMed:11416169).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q9H1D9 | APBB2 Q92870-2 | 3 | EBI-710067, EBI-21535880 | |
BINARY | Q9H1D9 | ATPAF2 Q8N5M1 | 3 | EBI-710067, EBI-1166928 | |
BINARY | Q9H1D9 | EIF2S3 P41091 | 3 | EBI-710067, EBI-1054228 | |
BINARY | Q9H1D9 | FKBP1A Q0VDC6 | 3 | EBI-710067, EBI-10226858 | |
BINARY | Q9H1D9 | GRN P28799 | 3 | EBI-710067, EBI-747754 | |
BINARY | Q9H1D9 | HSPA2 P54652 | 3 | EBI-710067, EBI-356991 | |
BINARY | Q9H1D9 | HSPB1 P04792 | 3 | EBI-710067, EBI-352682 | |
BINARY | Q9H1D9 | KIF1B O60333-2 | 3 | EBI-710067, EBI-10975473 | |
BINARY | Q9H1D9 | PMP22 A0A6Q8PF08 | 3 | EBI-710067, EBI-50433196 | |
BINARY | Q9H1D9 | PNRC1 Q12796 | 3 | EBI-710067, EBI-2827376 | |
BINARY | Q9H1D9 | POLR3C Q9BUI4 | 4 | EBI-710067, EBI-5452779 | |
BINARY | Q9H1D9 | POLR3G O15318 | 5 | EBI-710067, EBI-12362221 | |
BINARY | Q9H1D9 | POLR3GL Q9BT43 | 8 | EBI-710067, EBI-2855862 | |
BINARY | Q9H1D9 | PRPF4B Q13523 | 2 | EBI-710067, EBI-395940 | |
BINARY | Q9H1D9 | PRPS1 P60891 | 3 | EBI-710067, EBI-749195 | |
BINARY | Q9H1D9 | WFS1 O76024 | 3 | EBI-710067, EBI-720609 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Domain
The [4FE-4S] cluster-binding domain adopts a globular structure that serves as an interaction hub that connects the POLR3C/RPC3-POLR3F/RPC6-POLR3G/RPC7 heterotrimer to the Pol III core.
Sequence similarities
Belongs to the eukaryotic RPC34/RPC39 RNA polymerase subunit family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length316
- Mass (Da)35,684
- Last updated2001-03-01 v1
- Checksum49B1360AF8B365ED
Computationally mapped potential isoform sequences
There are 14 potential isoforms mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
Q05DB8 | Q05DB8_HUMAN | POLR3F | 275 | ||
A0A8V8TMS5 | A0A8V8TMS5_HUMAN | POLR3F | 50 | ||
A0A8V8TMT0 | A0A8V8TMT0_HUMAN | POLR3F | 244 | ||
A0A8V8TMI8 | A0A8V8TMI8_HUMAN | POLR3F | 204 | ||
A0A8V8TMJ7 | A0A8V8TMJ7_HUMAN | POLR3F | 42 | ||
A0A8V8TMS0 | A0A8V8TMS0_HUMAN | POLR3F | 268 | ||
A0A8V8TL45 | A0A8V8TL45_HUMAN | POLR3F | 120 | ||
A0A8V8TL49 | A0A8V8TL49_HUMAN | POLR3F | 37 | ||
A0A8V8TL53 | A0A8V8TL53_HUMAN | POLR3F | 232 | ||
A0A8V8TL66 | A0A8V8TL66_HUMAN | POLR3F | 323 | ||
A0A8V8TL69 | A0A8V8TL69_HUMAN | POLR3F | 168 | ||
A0A8V8TL74 | A0A8V8TL74_HUMAN | POLR3F | 168 | ||
A0A8V8TLI4 | A0A8V8TLI4_HUMAN | POLR3F | 348 | ||
A0A8V8TLJ3 | A0A8V8TLJ3_HUMAN | POLR3F | 86 |
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 2 | in Ref. 1; AAB63677 | ||||
Sequence: A → G | ||||||
Sequence conflict | 44-53 | in Ref. 1; AAB63677 | ||||
Sequence: HIEAQQRAVA → QYRSPAAGSS | ||||||
Sequence conflict | 255-290 | in Ref. 1; AAB63677 | ||||
Sequence: AKEGTVGSVDGHMKLYRAVNPIIPPTGLVRAPCGLC → CKRRHSWQCRWTHETVQGSQSNHPSHRFGPGHPVDSA |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
U93869 EMBL· GenBank· DDBJ | AAB63677.1 EMBL· GenBank· DDBJ | mRNA | ||
AK290892 EMBL· GenBank· DDBJ | BAF83581.1 EMBL· GenBank· DDBJ | mRNA | ||
AL121893 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CH471133 EMBL· GenBank· DDBJ | EAX10240.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BC012588 EMBL· GenBank· DDBJ | AAH12588.1 EMBL· GenBank· DDBJ | mRNA |