Domain ID e4by1A5

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  • A: beta barrels
  • X: cradle loop barrel
  • H: RIFT-related
  • T: double psi
  • F: RNA_pol_Rpb1_2
UID: 001385875
Type: Automatic domain
Parent: e1twfA1
Range: A:337-374,A:436-519
Ligands: APC MG
PDB: 4by1
PDB Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
UniProt: P04050
Hsap BLAST neighbor: P24928
Species: Saccharomyces cerevisiae

Structure of domain e4by1A5

Domains in the same chain:

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e4by1A4 A:2-336 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
e4by1A5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e4by1A2 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
e4by1A9 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
e4by1A3 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
e4by1A7 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
e4by1A1 A:1060-1102,A:1301-1455 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
e4by1A6 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
e4by1A8 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:

e4by1A4 A:2-336 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
e4by1A5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e4by1A2 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
e4by1A9 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
e4by1A3 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
e4by1A7 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
e4by1A1 A:1060-1102,A:1301-1455 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
e4by1A6 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
e4by1A8 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
e4by1B5 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
e4by1B1 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
e4by1B7 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
e4by1B6 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
e4by1B3 B:814-850,B:975-1097 cradle loop barrel RIFT-related double psi
e4by1B2 B:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4by1B4 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
e4by1C3 C:3-41,C:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4by1C4 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
e4by1D1 D:4-71,D:131-221 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e4by1E2 E:2-143 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e4by1E1 E:144-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e4by1F1 F:71-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e4by1G1 G:1-68 Dodecin subunit-like Flavin-binding protein dodecin-like Flavin-binding protein dodecin-like
e4by1G2 G:69-171 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4by1H1 H:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4by1I2 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by1I1 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by1J1 J:1-65 HTH RPB10 RPB10
e4by1K1 K:1-115 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4by1L1 L:25-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4by1X1 X:232-365 RuvA-C Elongation factor TFIIS domain 2/ Kix domain of creb binding protein Elongation factor TFIIS domain 2/ Kix domain of creb binding protein

Structural contacts of domain e4by1A5 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
e4by1B3 A:X,Y,Z->B:x,y,z RIFT-related Interaction Interface Pymol
e4by1B4 A:X,Y,Z->B:x,y,z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e4by1F1 A:X,Y,Z->F:x,y,z RPB6/omega subunit-like Interaction Interface Pymol
e4by1K1 A:X,Y,Z->K:x,y,z RBP11-like subunits of RNA polymerase Interaction Interface Pymol
e4by1K1 A:X,Y,Z->G:x,y,z RBP11-like subunits of RNA polymerase Interaction Interface Pymol