Domain ID e1smyD9

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  • A: a+b complex topology
  • X: N-terminal domain in RNA-polymerase beta-prime subunit
  • H: N-terminal domain in RNA-polymerase beta-prime subunit
  • T: N-terminal domain in RNA-polymerase beta-prime subunit
  • F: RNA_pol_Rpb1_1
UID: 001826670
Type: Automatic domain
Parent: e2a69D1
Range: D:2-165,D:449-610
Ligands: MG ZN
PDB: 1smy
PDB Description: DNA-DIRECTED RNA POLYMERASE BETA' CHAIN
UniProt: Q8RQE8
Hsap BLAST neighbor: P24928
Species: Thermus thermophilus

Structure of domain e1smyD9

Domains in the same chain:

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e1smyD9 D:2-165,D:449-610 N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit
e1smyD5 D:166-217,D:364-394 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyD1 D:395-448 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyD2 D:611-653,D:697-777 cradle loop barrel RIFT-related double psi
e1smyD7 D:654-696 inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit
e1smyD8 D:778-948 first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit
e1smyD3 D:949-1109 second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit
e1smyD4 D:1110-1200 MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e1smyD10 D:1201-1269,D:1331-1505 central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit
e1smyD6 D:1270-1330 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif

Domains in the same PDB:

e1smyA1 A:1-49,A:173-227 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1smyA2 A:50-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e1smyB1 B:1-49,B:173-227 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1smyB2 B:50-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e1smyC4 C:1-142,C:332-457 N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1smyC5 C:143-331 insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase
e1smyC2 C:458-591 barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase
e1smyC6 C:592-662 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyC8 C:663-700,C:834-999 cradle loop barrel RIFT-related double psi
e1smyC9 C:701-833 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyC7 C:1000-1119 C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1smyD9 D:2-165,D:449-610 N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit
e1smyD5 D:166-217,D:364-394 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyD1 D:395-448 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyD2 D:611-653,D:697-777 cradle loop barrel RIFT-related double psi
e1smyD7 D:654-696 inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit
e1smyD8 D:778-948 first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit
e1smyD3 D:949-1109 second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit
e1smyD4 D:1110-1200 MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e1smyD10 D:1201-1269,D:1331-1505 central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit
e1smyD6 D:1270-1330 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyE1 E:2-96 RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit
e1smyF3 F:78-257 Sigma2 domain-like Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors
e1smyF1 F:258-317 HTH HTH tri-helical
e1smyF2 F:319-423 HTH HTH tri-helical
e1smyK1 K:1-49,K:173-227 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1smyK2 K:50-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e1smyL1 L:1-49,L:173-227 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1smyL2 L:50-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e1smyM4 M:1-141,M:331-456 N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1smyM5 M:142-330 insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase
e1smyM6 M:458-591 barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase
e1smyM2 M:592-662 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyM9 M:664-700,M:827-999 cradle loop barrel RIFT-related double psi
e1smyM8 M:699-832 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyM7 M:999-1118 C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1smyN9 N:2-165,N:449-610 N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit
e1smyN8 N:166-217,N:364-394 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyN6 N:395-448 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyN4 N:611-653,N:697-777 cradle loop barrel RIFT-related double psi
e1smyN2 N:654-696 inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit
e1smyN1 N:778-948 first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit
e1smyN10 N:949-1109 second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit
e1smyN7 N:1110-1200 MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e1smyN3 N:1201-1269,N:1331-1505 central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit
e1smyN5 N:1270-1330 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1smyO1 O:2-96 RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit
e1smyP3 P:78-257 Sigma2 domain-like Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors
e1smyP1 P:258-317 HTH HTH tri-helical
e1smyP2 P:319-423 HTH HTH tri-helical

Structural contacts of domain e1smyD9 of H-group "N-terminal domain in RNA-polymerase beta-prime subunit":

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The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain IDSymmetry operatorH-groupVisualization
e1smyC9 D:x,y,z->C:X,Y,Z alpha/beta-Hammerhead/Barrel-sandwich hybrid Interaction Interface Pymol
e1smyC7 D:x,y,z->C:X,Y,Z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e1smyF2 D:X,Y,Z->F:x,y,z HTH Interaction Interface Pymol
e1smyF1 D:X,Y,Z->F:x,y,z HTH Interaction Interface Pymol
e1smyF3 D:X,Y,Z->F:x,y,z Sigma2 domain of RNA polymerase sigma factors Interaction Interface Pymol
e1smyL2 D:X,Y-1,Z->L:x,y,z Insert subdomain of RNA polymerase alpha subunit Interaction Interface Pymol