› 357d

X-ray diffraction
3.5Å resolution

3.5 A structure of fragment I from E. coli 5S RRNA

Released:
DOI: 10.2210/pdb357d/pdb
PDB entry 357d coloured by chain, front view.
PDB entry 357d coloured by chain, side view.
PDB entry 357d coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
Correll CC, Freeborn B, Moore PB, Steitz TA
Cell 91 705-12 (1997)
PMID: 9393863

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196616 (preferred)
Entry contents:
3 distinct RNA molecules
Macromolecules (3 distinct):
RNA-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 11 nucleotides
Theoretical weight: 3.51 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G*UP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 19 nucleotides
Theoretical weight: 6.17 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP* GP*CP*CP*AP*GP*GP*CP*AP*U)-3') Chain: C
Molecule details ›
Chain: C
Length: 31 nucleotides
Theoretical weight: 10.01 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand MG 8 x MG
Ligand HG 1 x HG
1 modified residue:
Ligand SSU 1 x SSU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P6122
Unit cell:
a: 58.67Å b: 58.67Å c: 248.84Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.312 0.312 0.265
Expression system: Escherichia coli

Quick links

Citations

45 review citations

How RNA folds.
Tinoco et al. (1999)
44 more

1 mention without citation

Predicting the Animal Susceptibility and Therapeutic Drugs to SARS-CoV-2 Based on Spike Glycoprotein Combined With ACE2.
Shen et al. (2020)