2PPB
Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
G [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
G [auth A] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
G [auth A] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2021-05-27) |
H [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
H [auth B] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2021-05-27) |
H [auth B] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
L [auth K] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2021-05-27) |
L [auth K] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
L [auth K] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
M [auth L] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2021-05-27) |
M [auth L] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
M [auth L] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2021-05-27) |
I [auth C] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2021-05-27) |
I [auth C] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2021-05-27) |
N [auth M] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2021-05-27) |
N [auth M] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2021-05-27) |
J [auth D] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039613 | 3001330 | SCOP2B (2021-05-27) |
O [auth N] | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039613 | 3001330 | SCOP2B (2021-05-27) |
K [auth E] | SCOP2B Superfamily | RPB6/omega subunit-like | 8039612 | 3000189 | SCOP2B (2021-05-27) |
P [auth O] | SCOP2B Superfamily | RPB6/omega subunit-like | 8039612 | 3000189 | SCOP2B (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
G [auth A] | PF01193 | e2ppbA1 | 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: PF01193 | ECOD (1.6) |
G [auth A] | PF01000 | e2ppbA2 | 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: PF01000 | ECOD (1.6) |
H [auth B] | PF01193 | e2ppbB1 | 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: PF01193 | ECOD (1.6) |
H [auth B] | PF01000 | e2ppbB2 | 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: PF01000 | ECOD (1.6) |
L [auth K] | PF01193 | e2ppbK1 | 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: PF01193 | ECOD (1.6) |
L [auth K] | PF01000 | e2ppbK2 | 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: PF01000 | ECOD (1.6) |
M [auth L] | PF01193 | e2ppbL1 | 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: PF01193 | ECOD (1.6) |
M [auth L] | PF01000 | e2ppbL2 | 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: PF01000 | ECOD (1.6) |
I [auth C] | PF00562 | e2ppbC9 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00562 | ECOD (1.6) |
I [auth C] | F_UNCLASSIFIED | e2ppbC2 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: F_UNCLASSIFIED | ECOD (1.6) |
I [auth C] | PF00562 | e2ppbC8 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: PF00562 | ECOD (1.6) |
I [auth C] | PF04563,PF04565 | e2ppbC4 | 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: PF04563,PF04565 | ECOD (1.6) |
I [auth C] | PF04561 | e2ppbC5 | 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: PF04561 | ECOD (1.6) |
I [auth C] | PF10385 | e2ppbC6 | 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: PF10385 | ECOD (1.6) |
I [auth C] | PF00562,PF04560 | e2ppbC7 | 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: PF00562,PF04560 | ECOD (1.6) |
N [auth M] | PF00562 | e2ppbM9 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00562 | ECOD (1.6) |
N [auth M] | F_UNCLASSIFIED | e2ppbM2 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: F_UNCLASSIFIED | ECOD (1.6) |
N [auth M] | PF00562 | e2ppbM8 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: PF00562 | ECOD (1.6) |
N [auth M] | PF04563,PF04565 | e2ppbM4 | 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: PF04563,PF04565 | ECOD (1.6) |
N [auth M] | PF04561 | e2ppbM5 | 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: PF04561 | ECOD (1.6) |
N [auth M] | PF10385 | e2ppbM6 | 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: PF10385 | ECOD (1.6) |
N [auth M] | PF00562,PF04560 | e2ppbM7 | 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: PF00562,PF04560 | ECOD (1.6) |
J [auth D] | PF00623 | e2ppbD9 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00623 | ECOD (1.6) |
J [auth D] | F_UNCLASSIFIED | e2ppbD10 | A: alpha arrays | X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology) | H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology) | T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit | F: F_UNCLASSIFIED | ECOD (1.6) |
J [auth D] | F_UNCLASSIFIED | e2ppbD8 | 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: F_UNCLASSIFIED | ECOD (1.6) |
J [auth D] | F_UNCLASSIFIED | e2ppbD1 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: F_UNCLASSIFIED | ECOD (1.6) |
J [auth D] | PF04997 | e2ppbD3 | 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: PF04997 | ECOD (1.6) |
J [auth D] | PF04998 | e2ppbD4 | 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: PF04998 | ECOD (1.6) |
J [auth D] | PF04998,PF05000 | e2ppbD5 | 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: PF04998,PF05000 | ECOD (1.6) |
J [auth D] | PF04983 | e2ppbD6 | 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: PF04983 | ECOD (1.6) |
O [auth N] | PF00623 | e2ppbN2 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: PF00623 | ECOD (1.6) |
O [auth N] | F_UNCLASSIFIED | e2ppbN4 | A: alpha arrays | X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology) | H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology) | T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit | F: F_UNCLASSIFIED | ECOD (1.6) |
O [auth N] | F_UNCLASSIFIED | e2ppbN40 | 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: F_UNCLASSIFIED | ECOD (1.6) |
O [auth N] | F_UNCLASSIFIED | e2ppbN39 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: F_UNCLASSIFIED | ECOD (1.6) |
O [auth N] | PF04997 | e2ppbN37 | 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: PF04997 | ECOD (1.6) |
O [auth N] | PF04998 | e2ppbN42 | 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: PF04998 | ECOD (1.6) |
O [auth N] | PF04998,PF05000 | e2ppbN41 | 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: PF04998,PF05000 | ECOD (1.6) |
O [auth N] | PF04983 | e2ppbN35 | 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: PF04983 | ECOD (1.6) |
K [auth E] | PF01192 | e2ppbE1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RNA polymerase omega subunit | F: PF01192 | ECOD (1.6) |
P [auth O] | PF01192 | e2ppbO1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RNA polymerase omega subunit | F: PF01192 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
G [auth A], H [auth B], L [auth K], M [auth L] | 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 |
G [auth A], H [auth B], L [auth K], M [auth L] | 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 |
I [auth C], N [auth M] | 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 |
I [auth C], N [auth M] | 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 |
I [auth C], N [auth M] | 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 |
I [auth C], N [auth M] | 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 |
I [auth C], N [auth M] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
I [auth C], N [auth M] | 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 |
J [auth D], O [auth N] | 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 |
J [auth D], O [auth N] | 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 |
J [auth D], O [auth N] | 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 |
J [auth D], O [auth N] | 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 |
J [auth D], O [auth N] | 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 |
K [auth E], P [auth O] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |