Domain ID e3h3vJ1

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  • A: few secondary structure elements
  • X: Rubredoxin-like
  • H: Rubredoxin-related
  • T: Rubredoxin-related
  • F: RNA_POL_M_15KD
UID: 000365752
Type: Automatic domain
Parent: e1twfI1
Range: J:2-49
Ligands: ZN
PDB: 3h3v
PDB Description: DNA-directed RNA polymerase II subunit RPB9
UniProt: P27999
Hsap BLAST neighbor: P36954
Species: Saccharomyces cerevisiae

Structure of domain e3h3vJ1

Domains in the same chain:

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e3h3vJ1 J:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e3h3vJ2 J:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Domains in the same PDB:

e3h3vB4 B: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
e3h3vB5 B:337-374,B:436-519 cradle loop barrel RIFT-related double psi
e3h3vB2 B: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
e3h3vB9 B: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
e3h3vB3 B: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
e3h3vB7 B: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
e3h3vB1 B:1060-1102,B: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
e3h3vB6 B:1103-1131,B: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
e3h3vB8 B: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
e3h3vC3 C:20-70,C:90-134,C:164-218,C: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
e3h3vC7 C: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
e3h3vC2 C: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
e3h3vC6 C: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
e3h3vC5 C:814-850,C:975-1097 cradle loop barrel RIFT-related double psi
e3h3vC4 C:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e3h3vC1 C: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
e3h3vD3 D:3-41,D:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e3h3vD4 D:42-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e3h3vE1 E:4-71,E:131-221 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e3h3vF2 F:2-142 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e3h3vF1 F:143-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e3h3vG1 G:72-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e3h3vH4 H:1-68 Dodecin subunit-like Flavin-binding protein dodecin-like Flavin-binding protein dodecin-like
e3h3vH3 H:69-171 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e3h3vI1 I:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e3h3vJ1 J:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e3h3vJ2 J:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e3h3vK1 K:1-65 HTH RPB10 RPB10
e3h3vL1 L:1-114 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e3h3vM1 M:25-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Structural contacts of domain e3h3vJ1 of H-group "Rubredoxin-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
e3h3vB6 J:x,y,z->B:X,Y,Z ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e3h3vB8 J:x,y,z->B:X,Y,Z permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e3h3vC7 J:x,y,z->C:X,Y,Z insertion domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e3h3vB7 J:X-1/2,-Y+1/2,-Z->B:x,y,z third helical domain in yeast RNA-polymerase II beta-prime subunit Interaction Interface Pymol