› 5k77

X-ray diffraction
2.17Å resolution

Dbr1 in complex with 7-mer branched RNA

Released:
DOI: 10.2210/pdb5k77/pdb
PDB entry 5k77 coloured by chain, front view.
PDB entry 5k77 coloured by chain, side view.
PDB entry 5k77 coloured by chain, top view.
Source organisms:
Primary publication:
Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.
Clark NE, Katolik A, Roberts KM, Taylor AB, Holloway SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick PF, Damha MJ, Hart PJ
Proc Natl Acad Sci U S A 113 14727-14732 (2016)
PMID: 27930312

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111330 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Lariat debranching enzyme Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 360 amino acids
Theoretical weight: 41.85 KDa
Source organism: Entamoeba histolytica
Expression system: Escherichia coli
UniProt:
  • Canonical: C4M1P9 (Residues: 1-354; Coverage: 100%)
Gene names: DBR1, EHI_062730
Sequence domains:
branch 1 of branched RNA 5'-UAA(-2'GU)CA-3' Chains: V, W, X, Y, Z
Molecule details ›
Chains: V, W, X, Y, Z
Length: 5 nucleotides
Theoretical weight: 1.55 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3' Chains: v, w, x, y, z
Molecule details ›
Chains: v, w, x, y, z
Length: 2 nucleotides
Theoretical weight: 606 Da
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 5 x ZN
Ligand FE2 5 x FE2
Ligand SO4 25 x SO4
Ligand OH 5 x OH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 73.151Å b: 141.892Å c: 212.511Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Strategies for Covalent Labeling of Long RNAs.
Depmeier et al. (2021)
1 more

2 mentions without citation

Artificial Metalloproteins: At the Interface between Biology and Chemistry.
Kerns et al. (2022)
1 more