› 1m5v

X-ray diffraction
2.4Å resolution

Transition State Stabilization by a Catalytic RNA

Released:
DOI: 10.2210/pdb1m5v/pdb
PDB entry 1m5v coloured by chain, front view.
PDB entry 1m5v coloured by chain, side view.
PDB entry 1m5v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Transition state stabilization by a catalytic RNA.
Rupert PB, Massey AP, Sigurdsson ST, Ferré-D'Amaré AR
Science 298 1421-4 (2002)
PMID: 12376595

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140462 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct RNA molecules
Macromolecules (4 distinct):
U1 small nuclear ribonucleoprotein A Chains: C, F
Molecule details ›
Chains: C, F
Length: 100 amino acids
Theoretical weight: 11.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 1-100; Coverage: 36%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
RNA INHIBITOR SUBSTRATE Chains: A, D
Molecule details ›
Chains: A, D
Length: 12 nucleotides
Theoretical weight: 3.87 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA INHIBITOR SUBSTRATE Chains: M, P
Molecule details ›
Chains: M, P
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA HAIRPIN RIBOZYME Chains: B, E
Molecule details ›
Chains: B, E
Length: 92 nucleotides
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Not provided
Sequence domains: Hairpin ribozyme 1 from viruses-like metatranscriptomes

Ligands and Environments

2 bound ligands:
Ligand CA 34 x CA
Ligand MPD 2 x MPD
1 modified residue:
Ligand A23 2 x A23

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 258.648Å b: 44.258Å c: 102.174Å
α: 90° β: 107.69° γ: 90°
R-values:
R R work R free
0.221 0.221 0.265
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

40 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
39 more

3 mentions without citation

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
Torelli et al. (2007)
2 more