› 8gxc

X-ray diffraction
2.5Å resolution

Crystal structure of NAD+ -II riboswitch in complex with NMN

Released:
DOI: 10.2210/pdb8gxc/pdb
PDB entry 8gxc coloured by chain, front view.
PDB entry 8gxc coloured by chain, side view.
PDB entry 8gxc coloured by chain, top view.
Source organisms:
Primary publication:
Structure-based investigations of the NAD+-II riboswitch.
Xu X, Egger M, Li C, Chen H, Micura R, Ren A
OpenAccess logo Nucleic Acids Res (2023)
PMID: 36610789

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140528 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chains: C, D, E, F, G
Molecule details ›
Chains: C, D, E, F, G
Length: 97 amino acids
Theoretical weight: 11.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 2-98; Coverage: 34%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
61-mer RNA Chains: A, B
Molecule details ›
Chains: A, B
Length: 61 nucleotides
Theoretical weight: 19.8 KDa
Source organism: Streptococcus sp.
Expression system: in vitro transcription vector pT7-TP(deltai)

Ligands and Environments

2 bound ligands:
Ligand NMN 2 x NMN
Ligand MG 16 x MG
1 modified residue:
Ligand GTP 2 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 57.588Å b: 122.677Å c: 154.378Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.269
Expression systems:
  • Escherichia coli
  • in vitro transcription vector pT7-TP(deltai)

Quick links

Citations

2 citation in other articles

Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.
Peng et al. (2023)
1 more

2 mentions without citation

trRosettaRNA: automated prediction of RNA 3D structure with transformer network.
Wang et al. (2023)
1 more