› 3r1h

X-ray diffraction
3.15Å resolution

Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound

Released:
DOI: 10.2210/pdb3r1h/pdb
PDB entry 3r1h coloured by chain, front view.
PDB entry 3r1h coloured by chain, side view.
PDB entry 3r1h coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structural basis of RNA-catalyzed RNA polymerization.
Shechner DM, Bartel DP
Nat Struct Mol Biol 18 1036-42 (2011)
PMID: 21857665

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140494 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
U1 small nuclear ribonucleoprotein A Chains: A, D
Molecule details ›
Chains: A, D
Length: 98 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09012 (Residues: 1-98; Coverage: 35%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
5'-R(*UP*CP*CP*AP*GP*UP*A)-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 7 nucleotides
Theoretical weight: 2.18 KDa
Source organism: Homo sapiens
Expression system: Not provided
Class I ligase ribozyme Chains: C, F
Molecule details ›
Chains: C, F
Length: 130 nucleotides
Theoretical weight: 42.1 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 26 x CA
2 modified residues:
Ligand GTP 2 x GTP
Ligand A23 2 x A23

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 58.69Å b: 70.011Å c: 71.858Å
α: 99.847° β: 99.735° γ: 103.651°
R-values:
R R work R free
0.212 0.212 0.255
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Progress toward synthetic cells.
Blain et al. (2014)
5 more

3 mentions without citation

The structural basis of RNA-catalyzed RNA polymerization.
Shechner et al. (2011)
2 more