1TWF

RNA polymerase II complexed with UTP at 2.3 A resolution


Domain Annotation: SCOP Classification SCOP Database (version: 2.0) Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpecies
Bd1twfb_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA-polymerase beta and beta-prime subunits of DNA dependent RNA-polymerase RNA-polymerase beta RBP2 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Cd1twfc1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RPB3 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Cd1twfc1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RPB3 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Cd1twfc2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RPB3 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Dd1twfe1 Alpha and beta proteins (a/b) Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Dd1twfe2 Alpha and beta proteins (a+b) RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5 Eukaryotic RPB5 C-terminal domain (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Ed1twff_ All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RPB6 RPB6 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Gd1twfi1 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Gd1twfi2 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Hd1twfj_ All alpha proteins DNA/RNA-binding 3-helical bundle RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Id1twfk_ Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RBP11/RpoL RPB11 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Jd1twfl_ Small proteins Rubredoxin-like RNA polymerase subunits RBP12 subunit of RNA polymerase II RBP12 subunit of RNA polymerase II (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Ad1twfa_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA-polymerase beta and beta-prime subunits of DNA dependent RNA-polymerase RNA-polymerase beta-prime RBP1 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
Fd1twfh_ All beta proteins OB-fold Nucleic acid-binding proteins RNA polymerase subunit RBP8 RNA polymerase subunit RBP8 (Saccharomyces cerevisiae ) [TaxId: 4932 ]
ChainDomainClassArchitectureTopologyHomology
B3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: B
B3.90.1070.20 Alpha Beta Alpha-Beta Complex Hypothetical Protein Ta0175 Chain: A, domain 2
B2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: B
B2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: B
B2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: B
B2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domain
B2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domain
B3.90.1800.10 Alpha Beta Alpha-Beta Complex DCoH-like RNA polymerase alpha subunit dimerisation domain
C3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2
C3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2
C2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2
D3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide Chain: A
D3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit
E3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omega
G2.20.25.10 Mainly Beta Single Sheet N-terminal domain of TfIIb
G2.20.25.10 Mainly Beta Single Sheet N-terminal domain of TfIIb
H1.10.10.60 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-like
I3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2
J2.20.28.30 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain L
A2.40.40.20 Mainly Beta Beta Barrel Barwin-like endoglucanases
A2.40.40.20 Mainly Beta Beta Barrel Barwin-like endoglucanases
A3.30.1490.180 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
A1.10.274.100 Mainly Alpha Orthogonal Bundle Enzyme I Chain A, domain 2
A1.10.132.30 Mainly Alpha Orthogonal Bundle Topoisomerase I Chain A, domain 4
A3.30.1360.140 Alpha Beta 2-Layer Sandwich Gyrase A domain 2
F2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
BPF04561RNA 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
BPF04560RNA 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
BPF04565RNA 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
BPF04566RNA 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
BPF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
BPF00562RNA 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
BPF04567RNA 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
CPF01193RNA 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
CPF01000RNA 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 archaealDomain
DPF01191RNA 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
DPF03871RNA 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
EPF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
GPF02150RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD)RNA polymerases M/15 Kd subunit- Domain
GPF01096Transcription factor S-II (TFIIS) (TFIIS_C)Transcription factor S-II (TFIIS)- Domain
HPF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
IPF13656RNA 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
JPF03604DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)DNA directed RNA polymerase, 7 kDa subunit- Domain
APF00623RNA 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
APF04990RNA 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
APF05001RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R)RNA polymerase Rpb1 C-terminal repeat- Repeat
APF05000RNA 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
APF04983RNA 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
APF04992RNA 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
APF04998RNA 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
APF04997RNA 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 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 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
FPF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
BDNA-directed RNA polymerase II 140 kDa polypeptide
CDNA-directed RNA polymerase II 45 kDa polypeptide
EDNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
FDNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
IDNA-directed RNA polymerase II 14.2 kDa polypeptide
JDNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
KDNA-directed RNA polymerase II 13.6 kDa polypeptide
LDNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
ADNA-directed RNA polymerase II largest subunit
HDNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide