7DY6
A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
I [auth F] | SCOP2B Superfamily | Sigma2 domain of RNA polymerase sigma factors | 8038503 | 3001393 | SCOP2B (2022-06-29) |
D [auth K] | SCOP2B Superfamily | C-terminal domain of RNA polymerase alpha subunit | 8042964 | 3000519 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
F [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
F [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
F [auth B] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
G [auth C] | RNA_pol_Rpb2_6_3rd | e7dy6C9 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd | ECOD (1.6) |
G [auth C] | PRK09603 | e7dy6C3 | A: a+b two layers | X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase | F: PRK09603 | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_6_2nd | e7dy6C2 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RNA_pol_Rpb2_6_2nd | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_6_1st | e7dy6C4 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RNA_pol_Rpb2_6_1st | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_6_2nd_2 | e7dy6C10 | A: a+b complex topology | X: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology) | H: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology) | T: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit | F: RNA_pol_Rpb2_6_2nd_2 | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_3 | e7dy6C1 | A: a+b complex topology | X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_3 | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_1 | e7dy6C7 | A: a+b complex topology | X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: insertion domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_1 | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_45 | e7dy6C8 | A: a+b complex topology | X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: barrel domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_45 | ECOD (1.6) |
G [auth C] | RNA_pol_Rpb2_7 | e7dy6C5 | A: a+b complex topology | X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_7 | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_2 | e7dy6D9 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb1_2 | ECOD (1.6) |
H [auth D] | PRK00566_2nd | e7dy6D5 | A: a+b two layers | X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology) | T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase | F: PRK00566_2nd | ECOD (1.6) |
H [auth D] | PRK14844 | e7dy6D3 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: PRK14844 | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_5_1st | e7dy6D7 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RNA_pol_Rpb1_5_1st | ECOD (1.6) |
H [auth D] | PRK00566_3rd,RNA_pol_Rpb1_5_3rd | e7dy6D1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: PRK00566_3rd,RNA_pol_Rpb1_5_3rd | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_1 | e7dy6D2 | A: a+b complex topology | X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology) | H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology) | T: N-terminal domain in RNA-polymerase beta-prime subunit | F: RNA_pol_Rpb1_1 | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_5_3rd | e7dy6D6 | A: a+b complex topology | X: central helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: central helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: central helical domain in RNA-polymerase beta-prime subunit | F: RNA_pol_Rpb1_5_3rd | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_4 | e7dy6D8 | A: a+b complex topology | X: second helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: second helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: second helical domain in RNA-polymerase beta-prime subunit | F: RNA_pol_Rpb1_4 | ECOD (1.6) |
H [auth D] | RNA_pol_Rpb1_3 | e7dy6D4 | A: a+b complex topology | X: first helical domain in RNA-polymerase beta-prime subunit (From Topology) | H: first helical domain in RNA-polymerase beta-prime subunit (From Topology) | T: first helical domain in RNA-polymerase beta-prime subunit | F: RNA_pol_Rpb1_3 | ECOD (1.6) |
I [auth F] | Sigma70_r3 | e7dy6F3 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Sigma70_r3 | ECOD (1.6) |
I [auth F] | Sigma70_r4 | e7dy6F2 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Sigma70_r4 | ECOD (1.6) |
I [auth F] | Sigma70_r2_2 | e7dy6F1 | A: alpha complex topology | X: Sigma2 domain-like | H: Sigma2 domain of RNA polymerase sigma factors (From Topology) | T: Sigma2 domain of RNA polymerase sigma factors | F: Sigma70_r2_2 | ECOD (1.6) |
K [auth E] | RNA_pol_Rpb6 | e7dy6E1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RNA polymerase omega subunit | F: RNA_pol_Rpb6 | ECOD (1.6) |
B [auth I] | GST_C_3 | e7dy6I2 | A: alpha superhelices | X: Repetitive alpha hairpins | H: Glutathione S-transferase (GST)-C (From Topology) | T: Glutathione S-transferase (GST)-C | F: GST_C_3 | ECOD (1.6) |
B [auth I] | GST_N | e7dy6I1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: GST_N | ECOD (1.6) |
C [auth J] | GST_C_3 | e7dy6J2 | A: alpha superhelices | X: Repetitive alpha hairpins | H: Glutathione S-transferase (GST)-C (From Topology) | T: Glutathione S-transferase (GST)-C | F: GST_C_3 | ECOD (1.6) |
C [auth J] | GST_N | e7dy6J1 | A: a+b three layers | X: Thioredoxin-like | H: Thioredoxin-like (From Topology) | T: Thioredoxin-like | F: GST_N | ECOD (1.6) |
D [auth K] | RNA_pol_A_CTD | e7dy6K1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: RNA_pol_A_CTD | ECOD (1.6) |
E [auth A] | RNA_pol_L | e7dy6A2 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L | ECOD (1.6) |
E [auth A] | RNA_pol_A_bac | e7dy6A1 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Insert subdomain of RNA polymerase alpha subunit (From Topology) | T: Insert subdomain of RNA polymerase alpha subunit | F: RNA_pol_A_bac | ECOD (1.6) |
F [auth B] | RNA_pol_L | e7dy6B2 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L | ECOD (1.6) |
F [auth B] | RNA_pol_A_bac | e7dy6B1 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Insert subdomain of RNA polymerase alpha subunit (From Topology) | T: Insert subdomain of RNA polymerase alpha subunit | F: RNA_pol_A_bac | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
G [auth C] | PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | 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 po ... | Domain |
G [auth C] | PF10385 | RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45) | RNA polymerase beta subunit external 1 domain | RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ... | Domain |
G [auth C] | PF04560 | RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7) | RNA polymerase Rpb2, domain 7 | 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 p ... | Domain |
G [auth C] | PF04565 | RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3) | RNA polymerase Rpb2, domain 3 | 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 ... | Domain |
G [auth C] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
G [auth C] | PF00562 | RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6) | RNA polymerase Rpb2, domain 6 | 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 ... | Domain |
H [auth D] | PF00623 | RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2) | RNA polymerase Rpb1, domain 2 | 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 ... | Domain |
H [auth D] | PF05000 | RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4) | RNA polymerase Rpb1, domain 4 | 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 do ... | Domain |
H [auth D] | PF04983 | RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3) | RNA polymerase Rpb1, domain 3 | 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 doma ... | Domain |
H [auth D] | PF04998 | RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5) | RNA polymerase Rpb1, domain 5 | 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 discontin ... | Domain |
H [auth D] | PF04997 | RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1) | RNA polymerase Rpb1, domain 1 | 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 do ... | Domain |
I [auth F] | PF04539 | Sigma-70 region 3 (Sigma70_r3) | Sigma-70 region 3 | - | Family |
I [auth F] | PF00140 | Sigma-70 factor, region 1.2 (Sigma70_r1_2) | Sigma-70 factor, region 1.2 | - | Family |
I [auth F] | PF04542 | Sigma-70 region 2 (Sigma70_r2) | Sigma-70 region 2 | Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ... | Domain |
I [auth F] | PF04545 | Sigma-70, region 4 (Sigma70_r4) | Sigma-70, region 4 | Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ... | Domain |
I [auth F] | PF04546 | Sigma-70, non-essential region (Sigma70_ner) | Sigma-70, non-essential region | The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. | Domain |
K [auth E] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
B [auth I], C [auth J] | PF00043 | Glutathione S-transferase, C-terminal domain (GST_C) | Glutathione S-transferase, C-terminal domain | GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins ... | Domain |
B [auth I], C [auth J] | PF02798 | Glutathione S-transferase, N-terminal domain (GST_N) | Glutathione S-transferase, N-terminal domain | Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity a ... | Domain |
D [auth K], E [auth A], F [auth B] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation 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 do ... | Domain |
D [auth K], E [auth A], F [auth B] | PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain |