Domain ID e4jk2D1

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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: 001124096
Type: Manual and representative domain
Range: D:8-333
Ligands: ZN
PDB: 4jk2
PDB Description: ESCHERICHIA COLI RNA POLYMERASE BETA' SUBUNIT
UniProt: P0A8T7
Hsap BLAST neighbor: P24928
Species:

Structure of domain e4jk2D1

Domains in the same chain:

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e4jk2D1 D:8-333 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
e4jk2D4 D:334-377,D:418-498 cradle loop barrel RIFT-related double psi
e4jk2D6 D:378-417 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
e4jk2D2 D:499-638 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
e4jk2D5 D:639-810 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
e4jk2D8 D:811-894 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
e4jk2D3 D:895-931,D:1135-1151,D:1216-1376 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
e4jk2D7 D:1152-1215 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif

Domains in the same PDB:

e4jk2A9 A:3-52,A:179-234 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4jk2A7 A:53-178 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4jk2A8 A:235-325 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e4jk2B4 B:6-52,B:174-236 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4jk2B3 B:53-173 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4jk2C3 C:8-152,C:450-577 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
e4jk2C10 C:153-226,C:343-451 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
e4jk2C1 C:227-234,C:289-342 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
e4jk2C8 C:235-288 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
e4jk2C9 C:578-714 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
e4jk2C4 C:713-790 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2C11 C:791-828,C:1058-1237 cradle loop barrel RIFT-related double psi
e4jk2C12 C:828-938 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2C5 C:939-1038 Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit
e4jk2C2 C:1238-1342 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
e4jk2D1 D:8-333 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
e4jk2D4 D:334-377,D:418-498 cradle loop barrel RIFT-related double psi
e4jk2D6 D:378-417 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
e4jk2D2 D:499-638 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
e4jk2D5 D:639-810 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
e4jk2D8 D:811-894 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
e4jk2D3 D:895-931,D:1135-1151,D:1216-1376 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
e4jk2D7 D:1152-1215 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2E1 E:2-91 RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit
e4jk2F4 F:6-52,F:174-234 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4jk2F3 F:53-173 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4jk2G4 G:6-52,G:174-232 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4jk2G3 G:53-173 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4jk2H3 H:8-152,H:450-577 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
e4jk2H10 H:153-226,H:343-451 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
e4jk2H1 H:227-234,H:289-342 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
e4jk2H8 H:235-288 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
e4jk2H9 H:578-714 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
e4jk2H4 H:713-790 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2H11 H:791-828,H:1058-1237 cradle loop barrel RIFT-related double psi
e4jk2H12 H:828-938 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2H5 H:939-1038 Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit
e4jk2H2 H:1238-1342 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
e4jk2I4 I:8-333 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
e4jk2I2 I:334-377,I:418-498 cradle loop barrel RIFT-related double psi
e4jk2I6 I:378-417 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
e4jk2I7 I:499-638 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
e4jk2I5 I:639-810 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
e4jk2I8 I:811-894 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
e4jk2I1 I:895-931,I:1135-1151,I:1216-1376 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
e4jk2I3 I:1152-1215 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4jk2J1 J:2-77 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e4jk2X1 X:6-64 RNA polymerase sigma factor rpoD N-terminal domain RNA polymerase sigma factor rpoD N-terminal domain RNA polymerase sigma factor rpoD N-terminal domain
e4jk2X2 X:95-154,X:212-446 Sigma2 domain-like Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors
e4jk2X4 X:447-507 HTH HTH tri-helical
e4jk2X3 X:508-609 HTH HTH tri-helical
e4jk2Y2 Y:95-154,Y:212-446 Sigma2 domain-like Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors
e4jk2Y1 Y:447-507 HTH HTH tri-helical
e4jk2Y3 Y:508-609 HTH HTH tri-helical

Structural contacts of domain e4jk2D1 of H-group "N-terminal domain in RNA-polymerase beta-prime subunit":

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
e4jk2C12 D:x,y,z->C:X,Y,Z alpha/beta-Hammerhead/Barrel-sandwich hybrid Interaction Interface Pymol
e4jk2C2 D:x,y,z->C:X,Y,Z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e4jk2X4 D:X,Y,Z->X:x,y,z HTH Interaction Interface Pymol
e4jk2X2 D:X,Y,Z->X:x,y,z Sigma2 domain of RNA polymerase sigma factors Interaction Interface Pymol
e4jk2X3 D:X,Y,Z->X:x,y,z HTH Interaction Interface Pymol
e4jk2X1 D:X,Y,Z->X:x,y,z RNA polymerase sigma factor rpoD N-terminal domain Interaction Interface Pymol
e4jk2C5 D:X-1/2,-Y+1/2,-Z->C:x,y,z Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit Interaction Interface Pymol
e4jk2Y2 D:-X-1,Y-1/2,-Z+1/2->Y:x,y,z Sigma2 domain of RNA polymerase sigma factors Interaction Interface Pymol
e4jk2I4 D:-X-1,Y-1/2,-Z+1/2->I:x,y,z N-terminal domain in RNA-polymerase beta-prime subunit Interaction Interface Pymol