› 3k0j

X-ray diffraction
3.1Å resolution

Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module

Released:
DOI: 10.2210/pdb3k0j/pdb
PDB entry 3k0j coloured by chain, front view.
PDB entry 3k0j coloured by chain, side view.
PDB entry 3k0j coloured by chain, top view.
Source organisms:
Primary publication:
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
Kulshina N, Edwards TE, Ferré-D'Amaré AR
RNA 16 186-96 (2010)
PMID: 19948769

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-140518 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 96 amino acids
Theoretical weight: 11.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 2-97; Coverage: 34%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
RNA (87-MER) Chains: E, F
Molecule details ›
Chains: E, F
Length: 87 nucleotides
Theoretical weight: 28.02 KDa
Source organism: Escherichia coli
Expression system: Not provided
Sequence domains: TPP riboswitch (THI element)

Ligands and Environments

2 bound ligands:
Ligand TPP 2 x TPP
Ligand MG 8 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 52.25Å b: 71.6Å c: 128.35Å
α: 90° β: 94.62° γ: 90°
R-values:
R R work R free
0.197 0.197 0.279
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Ribozymes and riboswitches: modulation of RNA function by small molecules.
Zhang et al. (2010)
9 more

9 mentions without citation

Long-Range Interactions in Riboswitch Control of Gene Expression.
Jones et al. (2017)
8 more