Domain ID e3m4oA6

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  • A: beta barrels
  • X: cradle loop barrel
  • H: RIFT-related
  • T: double psi
  • F: RNA_pol_Rpb1_2
UID: 001393835
Type: Automatic domain
Parent: e1twfA1
Range: A:337-374,A:436-519
Ligands: MG
PDB: 3m4o
PDB Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
UniProt: P04050
Hsap BLAST neighbor: P24928
Species: Saccharomyces cerevisiae

Structure of domain e3m4oA6

Domains in the same chain:

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e3m4oA3 A:3-336 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
e3m4oA6 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e3m4oA7 A:375-435 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
e3m4oA8 A:520-662 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
e3m4oA2 A:663-871 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
e3m4oA9 A:872-1059 helical domain in yeast RNA-polymerases third helical domain in yeast RNA-polymerase II beta-prime subunit third helical domain in yeast RNA-polymerase II beta-prime subunit
e3m4oA4 A:1060-1102,A:1301-1445 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
e3m4oA5 A:1103-1131,A:1243-1300 ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e3m4oA1 A:1132-1242 permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit

Domains in the same PDB:

e3m4oA3 A:3-336 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
e3m4oA6 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e3m4oA7 A:375-435 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
e3m4oA8 A:520-662 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
e3m4oA2 A:663-871 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
e3m4oA9 A:872-1059 helical domain in yeast RNA-polymerases third helical domain in yeast RNA-polymerase II beta-prime subunit third helical domain in yeast RNA-polymerase II beta-prime subunit
e3m4oA4 A:1060-1102,A:1301-1445 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
e3m4oA5 A:1103-1131,A:1243-1300 ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e3m4oA1 A:1132-1242 permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e3m4oB6 B:20-70,B:90-134,B:164-218,B:405-541 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
e3m4oB2 B:219-404 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
e3m4oB1 B:542-630 inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit
e3m4oB4 B:631-813 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
e3m4oB3 B:814-850,B:975-1097 cradle loop barrel RIFT-related double psi
e3m4oB7 B:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e3m4oB5 B:1098-1224 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
e3m4oC3 C:3-41,C:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e3m4oC4 C:42-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e3m4oE2 E:2-142 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e3m4oE1 E:143-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e3m4oF1 F:72-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e3m4oH1 H:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e3m4oI1 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e3m4oI2 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e3m4oJ1 J:1-65 HTH RPB10 RPB10
e3m4oK1 K:1-114 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e3m4oL1 L:25-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Structural contacts of domain e3m4oA6 of H-group "RIFT-related":

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
e3m4oB5 A:X,Y,Z->B:x,y,z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e3m4oB3 A:X,Y,Z->B:x,y,z RIFT-related Interaction Interface Pymol
e3m4oF1 A:X,Y,Z->F:x,y,z RPB6/omega subunit-like Interaction Interface Pymol
e3m4oK1 A:X,Y,Z->K:x,y,z RBP11-like subunits of RNA polymerase Interaction Interface Pymol