6RI7
Cryo-EM structure of E. coli RNA polymerase elongation complex bound to GreB transcription factor
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
D [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
D [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
D [auth A] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
E [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
E [auth B] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
E [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | 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) |
---|---|---|---|---|---|---|---|---|
C [auth F] | GreA_GreB_N | e6ri7F1 | A: alpha bundles | X: Long alpha-hairpin | H: GreA transcript cleavage protein, N-terminal domain (From Topology) | T: GreA transcript cleavage protein, N-terminal domain | F: GreA_GreB_N | ECOD (1.6) |
C [auth F] | GreA_GreB | e6ri7F2 | A: a+b two layers | X: FKBP-like | H: FKBP-like | T: FKBP-like | F: GreA_GreB | ECOD (1.6) |
J [auth G] | GreA_GreB_N | e6ri7G1 | A: alpha bundles | X: Long alpha-hairpin | H: GreA transcript cleavage protein, N-terminal domain (From Topology) | T: GreA transcript cleavage protein, N-terminal domain | F: GreA_GreB_N | ECOD (1.6) |
J [auth G] | GreA_GreB | e6ri7G2 | A: a+b two layers | X: FKBP-like | H: FKBP-like | T: FKBP-like | F: GreA_GreB | ECOD (1.6) |
D [auth A] | RNA_pol_L | e6ri7A2 | 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) |
D [auth A] | RNA_pol_A_bac | e6ri7A1 | 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) |
E [auth B] | RNA_pol_L | e6ri7B2 | 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 B] | RNA_pol_A_bac | e6ri7B1 | 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 C] | RNA_pol_Rpb2_6_3rd | e6ri7C10 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd | ECOD (1.6) |
F [auth C] | PRK09603 | e6ri7C6 | 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) |
F [auth C] | RNA_pol_Rpb2_6_2nd | e6ri7C8 | 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) |
F [auth C] | RNA_pol_Rpb2_6_1st | e6ri7C5 | 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) |
F [auth C] | RNA_pol_Rpb2_6_2nd_2 | e6ri7C2 | 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) |
F [auth C] | RNA_pol_Rpb2_3 | e6ri7C4 | 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) |
F [auth C] | RNA_pol_Rpb2_1 | e6ri7C7 | 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) |
F [auth C] | RNA_pol_Rpb2_45 | e6ri7C1 | 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) |
F [auth C] | RNA_pol_Rpb2_7 | e6ri7C9 | 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) |
G [auth D] | RNA_pol_Rpb1_2 | e6ri7D5 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb1_2 | ECOD (1.6) |
G [auth D] | PRK00566_2nd | e6ri7D1 | 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) |
G [auth D] | PRK14844 | e6ri7D8 | 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) |
G [auth D] | RNA_pol_Rpb1_5_1st | e6ri7D6 | 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) |
G [auth D] | PRK00566_3rd,RNA_pol_Rpb1_5_3rd | e6ri7D3 | 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) |
G [auth D] | RNA_pol_Rpb1_1 | e6ri7D9 | 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) |
G [auth D] | RNA_pol_Rpb1_5_3rd | e6ri7D2 | 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) |
G [auth D] | RNA_pol_Rpb1_4 | e6ri7D4 | 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) |
G [auth D] | RNA_pol_Rpb1_3 | e6ri7D7 | 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) |
H [auth E] | RNA_pol_Rpb6 | e6ri7E1 | 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) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
C [auth F], J [auth G] | PF03449 | Transcription elongation factor, N-terminal (GreA_GreB_N) | Transcription elongation factor, N-terminal | This domain adopts a long alpha-hairpin structure. | Domain |
C [auth F], J [auth G] | PF01272 | Transcription elongation factor, GreA/GreB, C-term (GreA_GreB) | Transcription elongation factor, GreA/GreB, C-term | This domain has an FKBP-like fold. | Domain |
D [auth A], E [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 A], E [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 |
F [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 |
F [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 |
F [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 |
F [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 |
F [auth C] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
F [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 |
G [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 |
G [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 |
G [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 |
G [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 E] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |