SMART: RNA_pol_Rpb6 domain annotation

RNA_pol_Rpb6 RNA polymerase Rpb6

SMART accession number:	SM01409
Description:	Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly PMID:11158566.
Interpro abstract (IPR006110):	In eukaryotes, there are three different forms of DNA-dependent RNA polymerases ( EC 2.7.7.6 ) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in Schizosaccharomyces pombe (Fission yeast) (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit. The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [ (PUBMED:11158566) ].
GO process:	transcription, DNA-templated (GO:0006351)
GO function:	DNA binding (GO:0003677), DNA-directed 5'-3' RNA polymerase activity (GO:0003899)
Family alignment:	View or

There are 0 RNA_pol_Rpb6 domains in 0 proteins in SMART's nrdb database.

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Cellular role (predicted cellular role)

Structure (3D structures containing this domain)

3D Structures of RNA_pol_Rpb6 domains in PDB

PDB code	Main view	Title
1hqm		CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA POLYMERASE-INCLUDES COMPLETE STRUCTURE WITH SIDE-CHAINS (EXCEPT FOR DISORDERED REGIONS)-FURTHER REFINED FROM ORIGINAL DEPOSITION-CONTAINS ADDITIONAL SEQUENCE INFORMATION
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
1i6v		THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX
1iw7		Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution
1k83		Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin
1l9u		THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION
1l9z		Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution
1nik		Wild Type RNA Polymerase II
1nt9		Complete 12-subunit RNA polymerase II
1pqv		RNA polymerase II-TFIIS complex
1qkl		hRPABC14.4, essential subunit of human RNA polymerases I, II and III
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
1smy		Structural basis for transcription regulation by alarmone ppGpp
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
1ynj		Taq RNA polymerase-Sorangicin complex
1ynn		Taq RNA polymerase-rifampicin complex
1zyr		Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin
2a68		Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin
2a69		Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin
2a6e		Crystal structure of the T. Thermophilus RNA polymerase holoenzyme
2a6h		Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin
2b63		Complete RNA Polymerase II-RNA inhibitor complex
2b8k		12-subunit RNA Polymerase II
2be5		Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin
2cw0		Crystal structure of Thermus thermophilus RNA polymerase holoenzyme at 3.3 angstroms resolution
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
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
2o5i		Crystal structure of the T. thermophilus RNA polymerase elongation complex
2o5j		Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog
2pmz		Archaeal RNA polymerase from Sulfolobus solfataricus
2ppb		Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
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
2waq		The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
2wb1		The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
2y0s		Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group
2yu9		RNA polymerase II elongation complex in 150 mm MG+2 with UTP
3aoh		RNA polymerase-Gfh1 complex (Crystal type 1)
3aoi		RNA polymerase-Gfh1 complex (Crystal type 2)
3cqz		Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
3dxj		Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin
3eql		Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic myxopyronin
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
3hkz		The X-ray crystal structure of RNA polymerase from Archaea
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
3iyd		Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
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
3lu0		Molecular model of Escherichia coli core RNA polymerase
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
3wod		RNA polymerase-gp39 complex
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
4ayb		RNAP at 3.2Ang
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
4g7h		Crystal structure of Thermus thermophilus transcription initiation complex
4g7o		Crystal structure of Thermus thermophilus transcription initiation complex containing 2 nt of RNA
4g7z		Crystal structure of Thermus thermophilus transcription initiation complex containing 5-BrU at template-strand position +1
4gzy		Crystal structures of bacterial RNA Polymerase paused elongation complexes
4gzz		Crystal structures of bacterial RNA Polymerase paused elongation complexes
4jk1		X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp)
4jk2		X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)
4jkr		Crystal Structure of E. coli RNA Polymerase in complex with ppGpp
4kmu		X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Rifampin
4kn4		X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2b
4kn7		X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c
4ljz		Crystal Structure Analysis of the E.coli holoenzyme
4lk0		Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex
4lk1		Crystal Structure Analysis of the E.coli holoenzyme
4llg		Crystal Structure Analysis of the E.coli holoenzyme/Gp2 complex
4mex		Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A
4mey		Crystal structure of Escherichia coli RNA polymerase holoenzyme
4mq9		Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077
4oin		Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077
4oio		Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation
4oip		Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP
4oiq		Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin
4oir		Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV
4q4z		4Q4Z
4q5s		4Q5S
4s20		4S20
4v1m		4V1M
4v1n		4V1N
4v1o		4V1O
4v8s		4V8S
4wqs		4WQS
4wqt		4WQT
4x67		4X67
4x6a		4X6A
4xln		4XLN
4xlp		4XLP
4xlq		4XLQ
4xlr		4XLR
4xls		4XLS
4xsx		4XSX
4xsy		4XSY
4xsz		4XSZ
4y52		4Y52
4y7n		4Y7N
4yfk		4YFK
4yfn		4YFN
4yfx		4YFX
4yg2		4YG2
4yln		4YLN
4ylo		4YLO
4ylp		4YLP
4ym7		4YM7
4zh2		4ZH2
4zh3		4ZH3
4zh4		4ZH4
5byh		5BYH
5c3e		5C3E
5c44		5C44
5c4a		5C4A
5c4j		5C4J
5c4x		5C4X
5d4c		5D4C
5d4d		5D4D
5d4e		5D4E
5e17		5E17
5e18		5E18
5ezk		5EZK
5fj8		5FJ8
5fj9		5FJ9
5fja		5FJA
5flm		5FLM
5fmf		5FMF
5fyw		5FYW
5fz5		5FZ5
5g5l		5G5L
5i2d		5I2D
5ip7		5IP7
5ip9		5IP9
5ipl		5IPL
5ipm		5IPM
5ipn		5IPN
5iy6		5IY6
5iy7		5IY7
5iy8		5IY8
5iy9		5IY9
5iya		5IYA
5iyb		5IYB
5iyc		5IYC
5iyd		5IYD
5m3f		5M3F
5m3m		5M3M
5sva		5SVA
5tmc		5TMC
5tmf		5TMF

Links (links to other resources describing this domain)

INTERPRO	IPR006110
PFAM	RNA_pol_Rpb6