› 3bo4

X-ray diffraction
3.33Å resolution

A relaxed active site following exon ligation by a group I intron

Released:
DOI: 10.2210/pdb3bo4/pdb
PDB entry 3bo4 coloured by chain, front view.
PDB entry 3bo4 coloured by chain, side view.
PDB entry 3bo4 coloured by chain, top view.
Source organisms:
Primary publication:
A relaxed active site after exon ligation by the group I intron.
Lipchock SV, Strobel SA
Proc Natl Acad Sci U S A 105 5699-704 (2008)
PMID: 18408159

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-113116 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
2 distinct DNA/RNA hybrid molecules
Macromolecules (4 distinct):
U1 small nuclear ribonucleoprotein A Chain: A
Molecule details ›
Chain: A
Length: 95 amino acids
Theoretical weight: 11.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09012 (Residues: 4-98; Coverage: 34%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Group I intron P9 Chain: B
Molecule details ›
Chain: B
Length: 197 nucleotides
Theoretical weight: 64.06 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*A)-D(P*DG)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 5.09 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA (5'-R(*CP*A)-D(P*DU)-R(P*AP*CP*GP*GP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 9 nucleotides
Theoretical weight: 2.83 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 12 x MG
Ligand K 6 x K
2 modified residues:
Ligand GTP 1 x GTP
Ligand A23 1 x A23

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P4122
Unit cell:
a: 111.188Å b: 111.188Å c: 240.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.281 0.28 0.296
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Structural insights into RNA splicing.
Toor et al. (2009)
2 more

2 mentions without citation

Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach.
Baba et al. (2016)
1 more