4OIP
Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8039604 | 3001655 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8039607 | 3001500 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | RPB6/omega subunit-like | 8039612 | 3000189 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Sigma factor domain-like | 8039614 | 3000953 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Sigma factor domain-like | 8039615 | 3000953 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Sigma2 domain of RNA polymerase sigma factors | 8039616 | 3001393 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039611 | 3001330 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Two-barrel nucleic acid polymerases | 8039613 | 3001330 | 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_L | e4oipA1 | 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) |
A | RNA_pol_A_bac | e4oipA2 | 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) |
B | RNA_pol_L | e4oipB2 | 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) |
B | RNA_pol_A_bac | e4oipB1 | 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 | RNA_pol_Rpb6 | e4oipE1 | 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) |
F | Sigma70_r3 | e4oipF3 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Sigma70_r3 | ECOD (1.6) |
F | Sigma70_r4 | e4oipF2 | A: alpha arrays | X: HTH | H: HTH | T: tri-helical | F: Sigma70_r4 | ECOD (1.6) |
F | Sigma70_r2_2 | e4oipF1 | 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) |
C | RNA_pol_Rpb2_6_3rd_3 | e4oipC8 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd_3 | ECOD (1.6) |
C | RNA_pol_Rpb2_6_1st_1 | e4oipC2 | 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_1 | ECOD (1.6) |
C | RNA_pol_Rpb2_6_2nd | e4oipC7 | 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) |
C | RNA_pol_Rpb2_3 | e4oipC3 | 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) |
C | RNA_pol_Rpb2_1 | e4oipC5 | 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) |
C | RNA_pol_Rpb2_45 | e4oipC1 | 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) |
C | RNA_pol_Rpb2_7 | e4oipC6 | 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) |
D | RNA_pol_Rpb1_2 | e4oipD7 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb1_2 | ECOD (1.6) |
D | PRK00566_1st | e4oipD3 | 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: PRK00566_1st | ECOD (1.6) |
D | PRK00566_2nd | e4oipD1 | 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) |
D | PRK00566_like | e4oipD9 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Duplicated hybrid motif | F: PRK00566_like | ECOD (1.6) |
D | biotinyl_domain_like | e4oipD5 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: biotinyl_domain_like | ECOD (1.6) |
D | RnfC_N_like_1 | e4oipD11 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RnfC_N_like_1 | ECOD (1.6) |
D | RNA_pol_Rpb1_5_2nd | e4oipD2 | 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_2nd | ECOD (1.6) |
D | Biotin_lipoyl_2_like | e4oipD6 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: Biotin_lipoyl_2_like | ECOD (1.6) |
D | RNA_pol_Rpb1_1 | e4oipD12 | 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) |
D | RNA_pol_Rpb1_5_3rd | e4oipD8 | 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) |
D | RNA_pol_Rpb1_4 | e4oipD4 | 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) |
D | RNA_pol_Rpb1_3 | e4oipD10 | 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) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 | |
PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family | |
PF04539 | Sigma-70 region 3 (Sigma70_r3) | Sigma-70 region 3 | - | Family | |
PF00140 | Sigma-70 factor, region 1.2 (Sigma70_r1_2) | Sigma-70 factor, region 1.2 | - | Family | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
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 | |
PF21668 | DNA-directed RNA polymerase subunit beta', hybrid domain (RPOC_hybrid) | DNA-directed RNA polymerase subunit beta', hybrid domain | This is a hybrid domain found in DNA-directed RNA polymerase subunit beta' (RPOC) found in Deinococcus [1-5]. | 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 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 |
0QZ | ||
2RA | Parent Component: ALA | |
2TL | ||
DSN | AA0195 , AA0624 :  D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 | :  |
DVA | AA0195 , AA0624 , AA0200 :  D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-valine MOD:00705 | :  |
FGL | Parent Component: GLY :  AA0195 , AA0624 , AA0200 , AA0185 , AA0458 :  D-serine (Ser) MOD:00202 , D-serine MOD:00891 , D-serine (Cys) MOD:00892 , 2-(L-cystein-S-yl)-D-serine MOD:01987 , D-valine MOD:00705 , L-3-oxoalanine (Cys) MOD:00193 , L-3-oxoalanine (Ser) MOD:00835 , L-3-oxoalanine MOD:01169 , aminomalonic acid (Ser) MOD:01384 | |
R2T | AA0195 , AA0624 , AA0200 , AA0185 , AA0458 | :