› 4peh

X-ray diffraction
2.1Å resolution

Dbr1 in complex with synthetic linear RNA

Released:
DOI: 10.2210/pdb4peh/pdb
PDB entry 4peh coloured by chain, front view.
PDB entry 4peh coloured by chain, side view.
PDB entry 4peh coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1.
Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ
Nucleic Acids Res 42 10845-55 (2014)
PMID: 25123664

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111328 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Lariat debranching enzyme Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 356 amino acids
Theoretical weight: 41.2 KDa
Source organism: Entamoeba histolytica
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: C4M1P9 (Residues: 1-354; Coverage: 100%)
Gene names: DBR1, EHI_062730
Sequence domains:
RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3') Chains: V, W, X, Y, Z
Molecule details ›
Chains: V, W, X, Y, Z
Length: 7 nucleotides
Theoretical weight: 2.27 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 5 x MN
Ligand SO4 8 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 73.021Å b: 141.936Å c: 212.942Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.203 0.247
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

7 review citations

Metallophosphoesterases: structural fidelity with functional promiscuity.
Matange et al. (2015)
6 more

8 mentions without citation

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs.
Islam et al. (2023)
7 more