Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.

Kettenberger, H., Armache, K.J., Cramer, P.

doi:10.1016/j.molcel.2004.11.040

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RNA Polymerase II-TFIIS-DNA/RNA complex

Annotation data related to this entry.

1Y1Y

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Domain Annotation: SCOP Classification (version 1.75)

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Domain Info	Class	Fold	Superfamily	Family	Domain	Species
d1y1ya_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yb_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yc_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yd_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1ye_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yf_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yg_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yh_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yi_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yj_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yk_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1yl_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
d1y1ys_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	Complete 12-subunit RNA polymerase II complex	Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Protein Family Annotation: Pfam Classification

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Chain	Pfam Accession	Pfam Family Identifier	Pfam Description	Type	Comment
B	PF00562	RNA_pol_Rpb2_6	RNA polymerase Rpb2, domain 6	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). Source: Pfam
J	PF01194	RNA_pol_N	RNA polymerases N / 8 kDa subunit	Domain	Source: Pfam
A	PF04997	RNA_pol_Rpb1_1	RNA polymerase Rpb1, domain 1	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, 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]. Source: Pfam
A	PF05000	RNA_pol_Rpb1_4	RNA polymerase Rpb1, domain 4	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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2]. Source: Pfam
B	PF04565	RNA_pol_Rpb2_3	RNA polymerase Rpb2, domain 3	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 3, s also known as the fork domain and is proximal to catalytic site [1]. Source: Pfam
B	PF04561	RNA_pol_Rpb2_2	RNA polymerase Rpb2, domain 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). 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). Source: Pfam
F	PF01192	RNA_pol_Rpb6	RNA polymerase Rpb6	Family
I	PF02150	RNA_POL_M_15KD	RNA polymerases M/15 Kd subunit	Domain	Source: Pfam
K	PF13656	RNA_pol_L_2	RNA polymerase Rpb3/Rpb11 dimerisation domain	Domain	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. Source: Pfam
K	PF01193	RNA_pol_L	RNA polymerase Rpb3/Rpb11 dimerisation domain	Domain	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. Source: Pfam
H	PF03870	RNA_pol_Rpb8	RNA polymerase Rpb8	Family
E	PF01191	RNA_pol_Rpb5_C	RNA polymerase Rpb5, C-terminal domain	Domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Source: Pfam
S	PF07500	TFIIS_M	Transcription factor S-II (TFIIS), central domain	Domain	Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and Pfam:PF01096 are required for transcription activity [1]. Source: Pfam
A	PF04983	RNA_pol_Rpb1_3	RNA polymerase Rpb1, domain 3	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, 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]. Source: Pfam
G	PF00575	S1	S1 RNA binding domain	Domain	The 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. Source: Pfam
A	PF04992	RNA_pol_Rpb1_6	RNA polymerase Rpb1, domain 6	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, 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. Source: Pfam
A	PF00623	RNA_pol_Rpb1_2	RNA polymerase Rpb1, domain 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). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2]. Source: Pfam
A	PF04990	RNA_pol_Rpb1_7	RNA polymerase Rpb1, domain 7	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, 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]. Source: Pfam
C	PF01193	RNA_pol_L	RNA polymerase Rpb3/Rpb11 dimerisation domain	Domain	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. Source: Pfam
B	PF04567	RNA_pol_Rpb2_5	RNA polymerase Rpb2, domain 5	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]. Source: Pfam
S	PF01096	TFIIS_C	Transcription factor S-II (TFIIS)	Domain	Source: Pfam
C	PF01000	RNA_pol_A_bac	RNA polymerase Rpb3/RpoA insert domain	Domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Source: Pfam
A	PF04998	RNA_pol_Rpb1_5	RNA polymerase Rpb1, domain 5	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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2]. Source: Pfam
L	PF03604	DNA_RNApol_7kD	DNA directed RNA polymerase, 7 kDa subunit	Domain	Source: Pfam
I	PF01096	TFIIS_C	Transcription factor S-II (TFIIS)	Domain	Source: Pfam
B	PF04566	RNA_pol_Rpb2_4	RNA polymerase Rpb2, domain 4	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]. Source: Pfam
D	PF03874	RNA_pol_Rpb4	RNA polymerase Rpb4	Family
G	PF03876	SHS2_Rpb7-N	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Domain	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]. Source: Pfam
B	PF04560	RNA_pol_Rpb2_7	RNA polymerase Rpb2, domain 7	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). 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]. Source: Pfam
B	PF04563	RNA_pol_Rpb2_1	RNA polymerase beta subunit	Family
G	PF08292	RNA_pol_Rbc25	RNA polymerase III subunit Rpc25	Domain	Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [1]. Source: Pfam
E	PF03871	RNA_pol_Rpb5_N	RNA polymerase Rpb5, N-terminal domain	Domain	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. Source: Pfam

Gene Product Annotation: GO Terms

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Polymer	Molecular Function	Biological Process	Cellular Component
5'-D(PTPAPCPGPCPCP*T)-3' (1Y1Y:T)	none	none	none
5'-R(PAPGPGPC)-3' (1Y1Y:P)	none	none	none
DNA-directed RNA polymerase II largest subunit (1Y1Y:A)	RNA polymerase II activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding transferase activity nucleotidyltransferase activity metal ion binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase II promoter translesion synthesis	nucleus DNA-directed RNA polymerase II, core complex
DNA-directed RNA polymerase II 140 kDa polypeptide (1Y1Y:B)	RNA polymerase II activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding transferase activity nucleotidyltransferase activity ribonucleoside binding metal ion binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase II promoter	nucleus DNA-directed RNA polymerase II, core complex
DNA-directed RNA polymerase II 45 kDa polypeptide (1Y1Y:C)	RNA polymerase II activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding metal ion binding protein dimerization activity	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase II promoter termination of RNA polymerase II transcription	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex
DNA-directed RNA polymerase II 32 kDa polypeptide (1Y1Y:D)	nucleotide binding single-stranded DNA binding single-stranded RNA binding catalytic activity DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding translation initiation factor binding	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay transcription, RNA-templated DNA repair transcription, DNA-templated transcription from RNA polymerase II promoter transcription initiation from RNA polymerase II promoter mRNA processing cellular response to DNA damage stimulus mRNA export from nucleus in response to heat stress recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex cellular metabolic process positive regulation of translational initiation	cytoplasmic mRNA processing body nucleus DNA-directed RNA polymerase II, core complex cytoplasm
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide (1Y1Y:E)	RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase I promoter transcription from RNA polymerase II promoter transcription from RNA polymerase III promoter ribosome biogenesis tRNA transcription from RNA polymerase III promoter	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex DNA-directed RNA polymerase III complex DNA-directed RNA polymerase I complex
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide (1Y1Y:F)	RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase I promoter transcription from RNA polymerase II promoter transcription from RNA polymerase III promoter ribosome biogenesis tRNA transcription from RNA polymerase III promoter	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex DNA-directed RNA polymerase III complex DNA-directed RNA polymerase I complex cytoplasm
DNA-directed RNA polymerase II 19 kDa polypeptide (1Y1Y:G)	single-stranded DNA binding RNA binding single-stranded RNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding translation initiation factor binding	nuclear-transcribed mRNA catabolic process, exonucleolytic transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase II promoter transcription initiation from RNA polymerase II promoter positive regulation of translational initiation positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	cytoplasmic mRNA processing body nucleus DNA-directed RNA polymerase II, core complex cytoplasm
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide (1Y1Y:H)	RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase I promoter transcription from RNA polymerase II promoter transcription from RNA polymerase III promoter ribosome biogenesis tRNA transcription from RNA polymerase III promoter	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex DNA-directed RNA polymerase III complex DNA-directed RNA polymerase I complex
DNA-directed RNA polymerase II subunit 9 (1Y1Y:I)	nucleic acid binding DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity zinc ion binding metal ion binding	transcription, RNA-templated maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter DNA repair transcription-coupled nucleotide-excision repair transcription, DNA-templated transcription from RNA polymerase II promoter transcription initiation from RNA polymerase II promoter cellular response to DNA damage stimulus	nucleus DNA-directed RNA polymerase II, core complex
DNA-directed RNA polymerases I/II/III subunit 10 (1Y1Y:J)	RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity zinc ion binding metal ion binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase I promoter transcription from RNA polymerase II promoter transcription from RNA polymerase III promoter ribosome biogenesis tRNA transcription from RNA polymerase III promoter	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex DNA-directed RNA polymerase III complex nucleolus DNA-directed RNA polymerase I complex
DNA-directed RNA polymerase II 13.6 kDa polypeptide (1Y1Y:K)	RNA polymerase II activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity protein binding protein dimerization activity	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase II promoter termination of RNA polymerase II transcription	nucleus DNA-directed RNA polymerase II, core complex
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide (1Y1Y:L)	RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity DNA binding DNA-directed RNA polymerase activity RNA-directed RNA polymerase activity zinc ion binding metal ion binding	transcription, RNA-templated transcription, DNA-templated transcription from RNA polymerase I promoter transcription from RNA polymerase II promoter transcription from RNA polymerase III promoter ribosome biogenesis tRNA transcription from RNA polymerase III promoter	nucleus nucleoplasm DNA-directed RNA polymerase II, core complex DNA-directed RNA polymerase III complex nucleolus DNA-directed RNA polymerase I complex
Transcription elongation factor S-II (1Y1Y:S)	nucleic acid binding zinc ion binding	transcription, DNA-templated regulation of transcription, DNA-templated regulation of transcription from RNA polymerase II promoter regulation of DNA-templated transcription, elongation	nucleus

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