RPOL8cRNA polymerase subunit 8 |
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| SMART accession number: | SM00658 |
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| Description: | subunit of RNA polymerase I, II and III |
| Interpro abstract (IPR005570): | Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits. |
| GO process: | transcription, DNA-templated (GO:0006351) |
| Family alignment: |
There are 1134 RPOL8c domains in 1133 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Taxonomic distribution of proteins containing RPOL8c domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RPOL8c domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing RPOL8c domain in the selected taxonomic class.
- Cellular role (predicted cellular role)
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Cellular role: transcription
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Cramer P, Bushnell DA, Kornberg RD
- Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
- Science. 2001; 292: 1863-76
- Display abstract
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
- Metabolism (metabolic pathways involving proteins which contain this domain)
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% proteins involved KEGG pathway ID Description 100.00 map03020 RNA polymerase This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RPOL8c domain which could be assigned to a KEGG orthologous group, and not all proteins containing RPOL8c domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
- Structure (3D structures containing this domain)
3D Structures of RPOL8c domains in PDB
PDB code Main view Title 1a1d 
YEAST RNA POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY 1i3q 
RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION 1i50 
RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION 1i6h 
RNA POLYMERASE II ELONGATION COMPLEX 1k83 
Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin 1nik 
Wild Type RNA Polymerase II 1nt9 
Complete 12-subunit RNA polymerase II 1pqv 
RNA polymerase II-TFIIS complex 1r5u 
RNA POLYMERASE II TFIIB COMPLEX 1r9s 
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE 1r9t 
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE 1sfo 
RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX 1twa 
RNA polymerase II complexed with ATP 1twc 
RNA polymerase II complexed with GTP 1twf 
RNA polymerase II complexed with UTP at 2.3 A resolution 1twg 
RNA polymerase II complexed with CTP 1twh 
RNA polymerase II complexed with 2'dATP 1wcm 
Complete 12-Subunit RNA Polymerase II at 3.8 A 1y1v 
Refined RNA Polymerase II-TFIIS complex 1y1w 
Complete RNA Polymerase II elongation complex 1y1y 
RNA Polymerase II-TFIIS-DNA/RNA complex 1y77 
Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP 2b63 
Complete RNA Polymerase II-RNA inhibitor complex 2b8k 
12-subunit RNA Polymerase II 2e2h 
RNA polymerase II elongation complex at 5 mM Mg2+ with GTP 2e2i 
RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP 2e2j 
RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP 2f3i 
Solution Structure of a Subunit of RNA Polymerase II 2ja5 
CPD lesion containing RNA Polymerase II elongation complex A 2ja6 
CPD lesion containing RNA Polymerase II elongation complex B 2ja7 
CPD lesion containing RNA Polymerase II elongation complex C 2ja8 
CPD lesion containing RNA Polymerase II elongation complex D 2nvq 
RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP 2nvt 
RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP 2nvx 
RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP 2nvy 
RNA Polymerase II form II in 150 mM Mn+2 2nvz 
RNA Polymerase II elongation complex with UTP, updated 11/2006 2r7z 
Cisplatin lesion containing RNA polymerase II elongation complex 2r92 
Elongation complex of RNA polymerase II with artificial RdRP scaffold 2r93 
Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop 2vum 
Alpha-amanitin inhibited complete RNA polymerase II elongation complex 2yu9 
RNA polymerase II elongation complex in 150 mm MG+2 with UTP 3cqz 
Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin 3fki 
12-Subunit RNA Polymerase II Refined with Zn-SAD data 3gtg 
Backtracked RNA polymerase II complex with 12mer RNA 3gtj 
Backtracked RNA polymerase II complex with 13mer RNA 3gtk 
Backtracked RNA polymerase II complex with 18mer RNA 3gtl 
Backtracked RNA polymerase II complex with 13mer with G<>U mismatch 3gtm 
Co-complex of Backtracked RNA polymerase II with TFIIS 3gto 
Backtracked RNA polymerase II complex with 15mer RNA 3gtp 
Backtracked RNA polymerase II complex with 24mer RNA 3gtq 
Backtracked RNA polymerase II complex induced by damage 3h0g 
RNA Polymerase II from Schizosaccharomyces pombe 3h3v 
Yeast RNAP II containing poly(A)-signal sequence in the active site 3hou 
Complete RNA polymerase II elongation complex I with a T-U mismatch 3hov 
Complete RNA polymerase II elongation complex II 3how 
Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine 3hox 
Complete RNA polymerase II elongation complex V 3hoy 
Complete RNA polymerase II elongation complex VI 3hoz 
Complete RNA polymerase II elongation complex IV with a T-U mismatch and a frayed RNA 3'-guanine 3i4m 
8-oxoguanine containing RNA polymerase II elongation complex D 3i4n 
8-oxoguanine containing RNA polymerase II elongation complex E 3j0k 
Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly 3j1n 
Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module 3k1f 
Crystal structure of RNA Polymerase II in complex with TFIIB 3k7a 
Crystal Structure of an RNA polymerase II-TFIIB complex 3m3y 
RNA polymerase II elongation complex C 3m4o 
RNA polymerase II elongation complex B 3po2 
Arrested RNA Polymerase II elongation complex 3po3 
Arrested RNA Polymerase II reactivation intermediate 3qt1 
RNA polymerase II variant containing A Chimeric RPB9-C11 subunit 3rzd 
RNA Polymerase II Initiation Complex with a 5-nt RNA 3rzo 
RNA Polymerase II Initiation Complex with a 4-nt RNA 3s14 
RNA Polymerase II Initiation Complex with a 6-nt RNA 3s15 
RNA Polymerase II Initiation Complex with a 7-nt RNA 3s16 
RNA Polymerase II Initiation Complex with an 8-nt RNA 3s17 
RNA Polymerase II Initiation Complex with a 9-nt RNA 3s1m 
RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 1) 3s1n 
RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2) 3s1q 
RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with ATP 3s1r 
RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP 3s2d 
RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U 3s2h 
RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP 4a3b 
RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid 4a3c 
RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid 4a3d 
RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid 4a3e 
RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP 4a3f 
RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with AMPCPP 4a3g 
RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid 4a3i 
RNA Polymerase II binary complex with DNA 4a3j 
RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with GMPCPP 4a3k 
RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid 4a3l 
RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP 4a3m 
RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with AMPCPP 4a93 
RNA Polymerase II elongation complex containing a CPD Lesion 4bbr 
Structure of RNA polymerase II-TFIIB complex 4bbs 
Structure of an initially transcribing RNA polymerase II-TFIIB complex 4bxx 
Structures of RNA polymerase II complexes with Bye1, a chromatin- binding PHF3 DIDO homologue 4bxz 
RNA Polymerase II-Bye1 complex 4by1 
elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP 4by7 
elongating RNA Polymerase II-Bye1 TLD complex 4c2m 
Structure of RNA polymerase I at 2.8 A resolution 4c3h 
Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93 4c3i 
Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100 4c3j 
Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90 4v1m 
4V1M 4v1n 
4V1N 4v1o 
4V1O 4x67 
4X67 4x6a 
4X6A 4y52 
4Y52 4y7n 
4Y7N 4ym7 
4YM7 5c3e 
5C3E 5c44 
5C44 5c4a 
5C4A 5c4j 
5C4J 5c4x 
5C4X 5fj8 
5FJ8 5fj9 
5FJ9 5fja 
5FJA 5flm 
5FLM 5fmf 
5FMF 5fyw 
5FYW 5fz5 
5FZ5 5g5l 
5G5L 5ip7 
5IP7 5ip9 
5IP9 5iy6 
5IY6 5iy7 
5IY7 5iy8 
5IY8 5iy9 
5IY9 5iya 
5IYA 5iyb 
5IYB 5iyc 
5IYC 5iyd 
5IYD 5m3f 
5M3F 5m3m 
5M3M 5sva 
5SVA - Links (links to other resources describing this domain)
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INTERPRO IPR005570