› 4pei

X-ray diffraction
1.95Å resolution

Dbr1 in complex with synthetic branched RNA analog

Released:
DOI: 10.2210/pdb4pei/pdb
PDB entry 4pei coloured by chain, front view.
PDB entry 4pei coloured by chain, side view.
PDB entry 4pei 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111329 (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: 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(*UP*AP*AP*CP*A)-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: synthetic construct
Expression system: Not provided
RNA (5'-R(*(G46)P*U)-3') Chains: Q, R, S, T, U
Molecule details ›
Chains: Q, R, S, T, U
Length: 2 nucleotides
Theoretical weight: 622 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand NI 5 x NI
Ligand SO4 5 x SO4
Ligand GOL 6 x GOL
Ligand PG4 1 x PG4
1 modified residue:
Ligand G46 5 x G46

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 73.037Å b: 142.479Å c: 214.665Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.229
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

7 review citations

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

2 mentions without citation

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.
Pires et al. (2016)
1 more