3CQZ
Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
External Resource: Annotation
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) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042682 | 3001330 | SCOP2B (2022-06-29) |
J [auth L] | SCOP2B Superfamily | RNA polymerase subunits | 8042695 | 3001823 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8042684 | 3001330 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042685 | 3001655 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8042687 | 3001500 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | Eukaryotic RPB5 N-terminal domain | 8044454 | 3000444 | SCOP2B (2022-06-29) |
D [auth E] | SCOP2B Superfamily | RPB5-like RNA polymerase subunit | 8035939 | 3001722 | SCOP2B (2022-06-29) |
E [auth F] | SCOP2B Superfamily | RPB6/omega subunit-like | 8042688 | 3000189 | SCOP2B (2022-06-29) |
F [auth H] | SCOP2B Superfamily | RBP8/CHS5 N-terminal domain-like | 8041967 | 3002702 | SCOP2B (2022-06-29) |
G [auth I] | SCOP2B Superfamily | Zinc beta-ribbon | 8042689 | 3001238 | SCOP2B (2022-06-29) |
G [auth I] | SCOP2B Superfamily | Zinc beta-ribbon | 8042690 | 3001238 | SCOP2B (2022-06-29) |
H [auth J] | SCOP2B Superfamily | RNA polymerase subunit RPB10 | 8042692 | 3001213 | SCOP2B (2022-06-29) |
I [auth K] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8042694 | 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) |
---|---|---|---|---|---|---|---|---|
A | RNA_pol_Rpb1_2 | e3cqzA8 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb1_2 | ECOD (1.6) |
A | RNA_pol_Rpb1_2_1 | e3cqzA7 | 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: RNA_pol_Rpb1_2_1 | ECOD (1.6) |
A | RNA_pol_Rpb1_7 | e3cqzA2 | A: a+b two layers | X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | F: RNA_pol_Rpb1_7 | ECOD (1.6) |
A | RNAP_II_Rpb1_C | e3cqzA4 | A: a+b two layers | X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology) | T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit | F: RNAP_II_Rpb1_C | ECOD (1.6) |
A | RNA_pol_Rpb1_1 | e3cqzA9 | 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) |
A | RNA_pol_Rpb1_5_3rd | e3cqzA3 | 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) |
A | RNA_pol_Rpb1_6 | e3cqzA5 | A: a+b complex topology | X: helical domain in yeast RNA-polymerases | H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology) | T: third helical domain in yeast RNA-polymerase II beta-prime subunit | F: RNA_pol_Rpb1_6 | ECOD (1.6) |
A | RNA_pol_Rpb1_4 | e3cqzA1 | 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) |
A | RNA_pol_Rpb1_3 | e3cqzA6 | 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) |
J [auth L] | DNA_RNApol_7kD | e3cqzL1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: DNA_RNApol_7kD | ECOD (1.6) |
B | RNA_pol_Rpb2_6_3rd_2 | e3cqzB6 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd_2 | ECOD (1.6) |
B | RNA_pol_Rpb2_6_2nd_1 | e3cqzB2 | 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_1 | ECOD (1.6) |
B | RNA_pol_Rpb2_3 | e3cqzB4 | 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) |
B | RNA_pol_Rpb2_1 | e3cqzB3 | 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) |
B | RNA_pol_Rpb2_45_1 | e3cqzB7 | 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_1 | ECOD (1.6) |
B | RNA_pol_Rpb2_7 | e3cqzB5 | 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) |
B | RNA_pol_Rpb2_4 | e3cqzB1 | A: a+b complex topology | X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | T: inserted a+b domain in yeast RNA polymerase beta subunit | F: RNA_pol_Rpb2_4 | ECOD (1.6) |
C | RNA_pol_L_1 | e3cqzC3 | 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_1 | ECOD (1.6) |
C | RNA_pol_A_bac_1 | e3cqzC4 | 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_1 | ECOD (1.6) |
D [auth E] | RNA_pol_Rpb5_C | e3cqzE1 | A: a+b two layers | X: RPB5-like RNA polymerase subunit (From Topology) | H: RPB5-like RNA polymerase subunit (From Topology) | T: RPB5-like RNA polymerase subunit | F: RNA_pol_Rpb5_C | ECOD (1.6) |
D [auth E] | RNA_pol_Rpb5_N | e3cqzE2 | A: a/b three-layered sandwiches | X: Restriction endonuclease-like | H: Eukaryotic RPB5 N-terminal domain (From Topology) | T: Eukaryotic RPB5 N-terminal domain | F: RNA_pol_Rpb5_N | ECOD (1.6) |
E [auth F] | RNA_pol_Rpb6_1 | e3cqzF1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: RNA_pol_Rpb6_1 | ECOD (1.6) |
F [auth H] | RNA_pol_Rpb8 | e3cqzH2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: RNA_pol_Rpb8 | ECOD (1.6) |
G [auth I] | RNA_POL_M_15KD | e3cqzI1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: RNA_POL_M_15KD | ECOD (1.6) |
G [auth I] | TFIIS_C | e3cqzI2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: TFIIS_C | ECOD (1.6) |
H [auth J] | RNA_pol_N | e3cqzJ1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: RNA_pol_N | ECOD (1.6) |
I [auth K] | RNA_pol_L_2 | e3cqzK1 | 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_2 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF04990 | RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7) | RNA polymerase Rpb1, 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). This domain, domain 7, represents a mobile modu ... | Domain | |
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 | |
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 | |
PF04992 | RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6) | RNA polymerase Rpb1, 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, domain 6, represents a mobile modu ... | Domain | |
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 | |
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 dom ... | Domain | |
J [auth L] | PF03604 | DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4) | DNA directed RNA polymerase, 7 kDa subunit | Domain | |
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 | |
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 | |
PF04566 | RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4) | RNA polymerase Rpb2, 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). Domain 4, is also known as the external 2 domain ... | Domain | |
PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family | |
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 | |
PF04567 | RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5) | RNA polymerase Rpb2, 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). Domain 5, is also known as the external 2 domain ... | Domain | |
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 | |
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 | |
D [auth E] | PF01191 | RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C) | RNA polymerase Rpb5, C-terminal domain | The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. | Domain |
D [auth E] | PF03871 | RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N) | RNA polymerase Rpb5, N-terminal 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 p ... | Domain |
E [auth F] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
F [auth H] | PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family |
G [auth I] | PF02150 | RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9) | RNA polymerases M/15 Kd subunit | Domain | |
G [auth I] | PF01096 | Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS) | Transcription factor S-II (TFIIS) | Domain | |
H [auth J] | PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | Domain | |
I [auth K] | PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2) | 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 |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
K [auth M] | CSX | Parent Component: CYS : AA0451 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 |
K [auth M] | HYP | Parent Component: PRO : AA0451 , AA0030 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039 |
K [auth M] | ILX | Parent Component: ILE : AA0451 , AA0030 , AA0449 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039 , (2S,3R,4R)-4,5-dihydroxyisoleucine MOD:01378 |
K [auth M] | TRX | Parent Component: TRP : AA0451 , AA0030 , AA0449 |