3HOU | pdb_00003hou

Complete RNA polymerase II elongation complex I with a T-U mismatch

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
X [auth U]SCOP2B SuperfamilyZinc beta-ribbon 8042689 3001238 SCOP2B (2022-06-29)
X [auth U]SCOP2B SuperfamilyZinc beta-ribbon 8042690 3001238 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon 8042689 3001238 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon 8042690 3001238 SCOP2B (2022-06-29)
W [auth T]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8041967 3002702 SCOP2B (2022-06-29)
W [auth T]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8093392 3002702 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8093392 3002702 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8041967 3002702 SCOP2B (2022-06-29)
V [auth S]SCOP2B SuperfamilyNucleic acid-binding proteins 8044251 3000135 SCOP2B (2022-06-29)
V [auth S]SCOP2B SuperfamilyN-terminal, heterodimerisation domain of RBP7 (RpoE) 8044252 3001137 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyNucleic acid-binding proteins 8044251 3000135 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyN-terminal, heterodimerisation domain of RBP7 (RpoE) 8044252 3001137 SCOP2B (2022-06-29)
U [auth R]SCOP2B SuperfamilyRPB6/omega subunit-like 8042688 3000189 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8042688 3000189 SCOP2B (2022-06-29)
T [auth Q]SCOP2B SuperfamilyRPB5-like RNA polymerase subunit 8035939 3001722 SCOP2B (2022-06-29)
T [auth Q]SCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain 8044454 3000444 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain 8044454 3000444 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRPB5-like RNA polymerase subunit 8035939 3001722 SCOP2B (2022-06-29)
R [auth O]SCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8042687 3001500 SCOP2B (2022-06-29)
R [auth O]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
R [auth O]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8042687 3001500 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
Q [auth N]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
Q [auth N]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8042695 3001823 SCOP2B (2022-06-29)
AA [auth X]SCOP2B SuperfamilyRNA polymerase subunits 8042695 3001823 SCOP2B (2022-06-29)
Z [auth W]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042694 3001655 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042694 3001655 SCOP2B (2022-06-29)
Y [auth V]SCOP2B SuperfamilyRNA polymerase subunit RPB10 8042692 3001213 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRNA polymerase subunit RPB10 8042692 3001213 SCOP2B (2022-06-29)
P [auth M]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042682 3001330 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042682 3001330 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
X [auth U]Ribosomal_L36e3houU1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
IRibosomal_L36e3houI1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
W [auth T]Ribosomal_L36e3houT1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
HRibosomal_L36e3houH1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
V [auth S]CAPe3houS3 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: CAPECOD (develop294)
GCAPe3houG3 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: CAPECOD (develop294)
U [auth R]Ribosomal_L36e3houR1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
FRibosomal_L36e3houF1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
T [auth Q]Ribosomal_L36e3houQ1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
ERibosomal_L36e3houE1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
S [auth P]Ribosomal_L36e3houP1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
DRibosomal_L36e3houD1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
R [auth O]DUF1254e3houO3 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: DUF1254ECOD (develop294)
CDUF1254e3houC3 A: alpha bundlesX: DEATH domainH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: DUF1254ECOD (develop294)
Q [auth N]EXOSC1e3houN1 A: alpha bundlesX: Anticodon-binding domain of Class II aaRSH: Anticodon-binding domain of Class II aaRST: Anticodon-binding domain of Class II aaRSF: EXOSC1ECOD (develop294)
BEXOSC1e3houB1 A: alpha bundlesX: Anticodon-binding domain of Class II aaRSH: Anticodon-binding domain of Class II aaRST: Anticodon-binding domain of Class II aaRSF: EXOSC1ECOD (develop294)
LRibosomal_L36e3houL1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
AA [auth X]Ribosomal_L36e3houX1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
Z [auth W]Ribosomal_L36e3houW1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
KRibosomal_L36e3houK1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
Y [auth V]Ribosomal_L36e3houV1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
JRibosomal_L36e3houJ1 A: alpha bundlesX: HTHH: HTHT: tetra-helical, lambda repressor-likeF: Ribosomal_L36ECOD (develop294)
P [auth M]ClpB_D2-smalle3houM1 A: alpha bundlesX: YrdC/RibBH: SH3T: SH3F: ClpB_D2-smallECOD (develop294)
AClpB_D2-smalle3houA1 A: alpha bundlesX: YrdC/RibBH: SH3T: SH3F: ClpB_D2-smallECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
X [auth U]2.20.25.10 Mainly Beta Single Sheet N-terminal domain of TfIIb CATH (4.3.0)
I2.20.25.10 Mainly Beta Single Sheet N-terminal domain of TfIIb CATH (4.3.0)
W [auth T]2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteinsCATH (4.3.0)
H2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteinsCATH (4.3.0)
V [auth S]3.30.1490.120 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
V [auth S]2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteinsCATH (4.3.0)
G3.30.1490.120 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (4.3.0)
G2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteinsCATH (4.3.0)
U [auth R]3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omegaCATH (4.3.0)
F3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omegaCATH (4.3.0)
T [auth Q]3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide Chain: ACATH (4.3.0)
T [auth Q]3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunitCATH (4.3.0)
E3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide Chain: ACATH (4.3.0)
E3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunitCATH (4.3.0)
S [auth P]1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone Chain: ACATH (4.3.0)
D1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone Chain: ACATH (4.3.0)
R [auth O]3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
R [auth O]2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
C3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
C2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
Q [auth N]3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
Q [auth N]3.90.1070.20 Alpha Beta Alpha-Beta Complex Hypothetical Protein Ta0175 Chain: A, domain 2CATH (4.3.0)
Q [auth N]2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
Q [auth N]2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domainCATH (4.3.0)
Q [auth N]3.90.1800.10 Alpha Beta Alpha-Beta Complex DCoH-like RNA polymerase alpha subunit dimerisation domainCATH (4.3.0)
B3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
B3.90.1070.20 Alpha Beta Alpha-Beta Complex Hypothetical Protein Ta0175 Chain: A, domain 2CATH (4.3.0)
B2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
B2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domainCATH (4.3.0)
B3.90.1800.10 Alpha Beta Alpha-Beta Complex DCoH-like RNA polymerase alpha subunit dimerisation domainCATH (4.3.0)
L2.20.28.30 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain LCATH (4.3.0)
AA [auth X]2.20.28.30 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain LCATH (4.3.0)
Z [auth W]3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
K3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
Y [auth V]1.10.10.60 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-likeCATH (4.3.0)
J1.10.10.60 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-likeCATH (4.3.0)
P [auth M]2.40.40.20 Mainly Beta Beta Barrel Barwin-like endoglucanases CATH (utative)
P [auth M]3.30.1490.180 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1CATH (utative)
P [auth M]1.10.274.100 Mainly Alpha Orthogonal Bundle Enzyme I Chain A, domain 2CATH (utative)
P [auth M]1.10.132.30 Mainly Alpha Orthogonal Bundle Topoisomerase I Chain A, domain 4CATH (utative)
P [auth M]3.30.1360.140 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (utative)
A3.30.1360.140 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I,
X [auth U]		PF02150RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunitDomain
I,
X [auth U]		PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)Domain
H,
W [auth T]		PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
G,
V [auth S]		PF03876SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].
Domain
G,
V [auth S]		PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Domain
F,
U [auth R]		PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
E,
T [auth Q]		PF01191RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)RNA polymerase Rpb5, C-terminal domainThe assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Domain
E,
T [auth Q]		PF03871RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)RNA polymerase Rpb5, N-terminal domainRpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.
Domain
D,
S [auth P]		PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family
C,
R [auth O]		PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Domain
C,
R [auth O]		PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Domain
B,
Q [auth N]		PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Domain
B,
Q [auth N]		PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].
Domain
B,
Q [auth N]		PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].
Domain
B,
Q [auth N]		PF04566RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)RNA polymerase Rpb2, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].
Domain
B,
Q [auth N]		PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
B,
Q [auth N]		PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Domain
B,
Q [auth N]		PF04567RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)RNA polymerase Rpb2, domain 5RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].
Domain
AA [auth X],
L		PF03604DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunitDomain
K,
Z [auth W]		PF13656RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.
Domain
J,
Y [auth V]		PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunitDomain
A,
P [auth M]		PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].
Domain
A,
P [auth M]		PF04990RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)RNA polymerase Rpb1, domain 7RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].
Domain
A,
P [auth M]		PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].
Domain
A,
P [auth M]		PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].
Domain
A,
P [auth M]		PF04992RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)RNA polymerase Rpb1, domain 6RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.
Domain
A,
P [auth M]		PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].
Domain
A,
P [auth M]		PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I,
X [auth U]		DNA-directed RNA polymerase II subunit RPB9
H,
W [auth T]		DNA-directed RNA polymerases I, II, and III subunit RPABC3
G,
V [auth S]		DNA-directed RNA polymerase II subunit RPB7
F,
U [auth R]		DNA-directed RNA polymerases I, II, and III subunit RPABC2
E,
T [auth Q]		DNA-directed RNA polymerases I, II, and III subunit RPABC1
D,
S [auth P]		DNA-directed RNA polymerase II subunit RPB4
C,
R [auth O]		DNA-directed RNA polymerase II subunit RPB3
B,
Q [auth N]		DNA-directed RNA polymerase II subunit RPB2
DA [auth 6],
O [auth 3]		5'-R(*UP*GP*CP*AP*UP*U*UP*CP*GP*AP*CP*CP*AP*GP*GP*CP*U)-3'---
CA [auth 5],
N [auth 2]		5'-D(*A*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3'---
BA [auth 4],
M [auth 1]		5'-D(*AP*GP*CP*TP*CP*A*AP*GP*TP*AP*GP*TP*TP*AP*TP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3'---
AA [auth X],
L		DNA-directed RNA polymerases I, II, and III subunit RPABC4
K,
Z [auth W]		DNA-directed RNA polymerase II subunit RPB11
J,
Y [auth V]		DNA-directed RNA polymerases I, II, and III subunit RPABC5
A,
P [auth M]		DNA-directed RNA polymerase II subunit RPB1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I,
X [auth U]		IPR001529DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbonDomain
I,
X [auth U]		IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
I,
X [auth U]		IPR001222Zinc finger, TFIIS-typeDomain
I,
X [auth U]		IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
I,
X [auth U]		IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
H,
W [auth T]		IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
H,
W [auth T]		IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
G,
V [auth S]		IPR003029S1 domainDomain
G,
V [auth S]		IPR045113RNA polymerase subunit Rpb7-likeFamily
G,
V [auth S]		IPR005576RNA polymerase Rpb7-like , N-terminalDomain
G,
V [auth S]		IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
G,
V [auth S]		IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
F,
U [auth R]		IPR028363DNA-directed RNA polymerase, subunit RPB6Family
F,
U [auth R]		IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
F,
U [auth R]		IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
F,
U [auth R]		IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
F,
U [auth R]		IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
E,
T [auth Q]		IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
E,
T [auth Q]		IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
E,
T [auth Q]		IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
E,
T [auth Q]		IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
E,
T [auth Q]		IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
E,
T [auth Q]		IPR005571RNA polymerase, Rpb5, N-terminalDomain
D,
S [auth P]		IPR005574RNA polymerase subunit Rpb4/RPC9Family
D,
S [auth P]		IPR010997HRDC-like superfamilyHomologous Superfamily
D,
S [auth P]		IPR006590RNA polymerase Rpb4/RPC9, coreDomain
D,
S [auth P]		IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
D,
S [auth P]		IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
C,
R [auth O]		IPR011262DNA-directed RNA polymerase, insert domainDomain
C,
R [auth O]		IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
C,
R [auth O]		IPR050518Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase SubunitFamily
C,
R [auth O]		IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
C,
R [auth O]		IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
C,
R [auth O]		IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
C,
R [auth O]		IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
B,
Q [auth N]		IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
B,
Q [auth N]		IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
B,
Q [auth N]		IPR007646RNA polymerase Rpb2, domain 4Domain
B,
Q [auth N]		IPR007647RNA polymerase Rpb2, domain 5Domain
B,
Q [auth N]		IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
B,
Q [auth N]		IPR007642RNA polymerase Rpb2, domain 2Domain
B,
Q [auth N]		IPR015712DNA-directed RNA polymerase, subunit 2Family
B,
Q [auth N]		IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
B,
Q [auth N]		IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
B,
Q [auth N]		IPR007645RNA polymerase Rpb2, domain 3Domain
B,
Q [auth N]		IPR007644RNA polymerase, beta subunit, protrusionDomain
B,
Q [auth N]		IPR007641RNA polymerase Rpb2, domain 7Domain
AA [auth X],
L		IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
AA [auth X],
L		IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
AA [auth X],
L		IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
K,
Z [auth W]		IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
K,
Z [auth W]		IPR037685RNA polymerase RBP11Family
K,
Z [auth W]		IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
K,
Z [auth W]		IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
K,
Z [auth W]		IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
J,
Y [auth V]		IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
J,
Y [auth V]		IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
J,
Y [auth V]		IPR023580RNA polymerase subunit RPB10Homologous Superfamily
A,
P [auth M]		IPR007081RNA polymerase Rpb1, domain 5Domain
A,
P [auth M]		IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
A,
P [auth M]		IPR007075RNA polymerase Rpb1, domain 6Domain
A,
P [auth M]		IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
A,
P [auth M]		IPR007083RNA polymerase Rpb1, domain 4Domain
A,
P [auth M]		IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
A,
P [auth M]		IPR006592RNA polymerase, N-terminalDomain
A,
P [auth M]		IPR007066RNA polymerase Rpb1, domain 3Domain
A,
P [auth M]		IPR007073RNA polymerase Rpb1, domain 7Domain
A,
P [auth M]		IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
A,
P [auth M]		IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
A,
P [auth M]		IPR000722RNA polymerase, alpha subunitDomain
A,
P [auth M]		IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
A,
P [auth M]		IPR007080RNA polymerase Rpb1, domain 1Domain