› 7eog

X-ray diffraction
1.5Å resolution

Crystal structure of the Pepper aptamer in complex with HBC, iridium hexammine soak

Released:
DOI: 10.2210/pdb7eog/pdb
PDB entry 7eog coloured by chain, front view.
PDB entry 7eog coloured by chain, side view.
PDB entry 7eog coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Structure-based investigation of fluorogenic Pepper aptamer.
Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A
Nat Chem Biol 17 1289-1295 (2021)
PMID: 34725509

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197236 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
Pepper (49-MER) Chain: A
Molecule details ›
Chain: A
Length: 48 nucleotides
Theoretical weight: 15.43 KDa
Source organism: synthetic construct
Expression system: in vitro transcription vector pT7-TP(deltai)

Ligands and Environments

4 bound ligands:
Ligand GTP 1 x GTP
Ligand J8F 1 x J8F
Ligand MG 5 x MG
Ligand IRI 3 x IRI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 92.925Å b: 34.771Å c: 58.552Å
α: 90° β: 128.11° γ: 90°
R-values:
R R work R free
0.193 0.192 0.218
Expression system: in vitro transcription vector pT7-TP(deltai)

Quick links

Citations

12 citation in other articles

RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair.
Sampedro Vallina et al. (2023)
11 more

2 mentions without citation

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.
Zirbel et al. (2022)
1 more