› 7d7v

X-ray diffraction
2.8Å resolution

Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein

Released:
DOI: 10.2210/pdb7d7v/pdb
Model geometry
Fit model/data
PDB entry 7d7v coloured by chain, front view.
PDB entry 7d7v coloured by chain, side view.
PDB entry 7d7v coloured by chain, top view.
Source organisms:
Primary publication:
Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A
OpenAccess logo Nucleic Acids Res 48 12394-12406 (2020)
PMID: 33170270

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-302185 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chain: C
Molecule details ›
Chain: C
Length: 92 amino acids
Theoretical weight: 10.68 KDa
Source organism: Homo sapiens
Expression system: bacterium
UniProt:
  • Canonical: P09012 (Residues: 5-96; Coverage: 33%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
17delU1A (58-MER) Chain: A
Molecule details ›
Chain: A
Length: 57 nucleotides
Theoretical weight: 18.27 KDa
Source organism: Acidobacterium capsulatum ATCC 51196
Expression system: in vitro transcription vector pT7-TP(deltai)
Sequence domains: nadA riboswitch

Ligands and Environments

3 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 8 x MG
Ligand NAD 1 x NAD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P6122
Unit cell:
a: 68.593Å b: 68.593Å c: 333.848Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.25 0.25 0.308
Expression systems:
  • bacterium
  • in vitro transcription vector pT7-TP(deltai)

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Citations

3 review citations

Discovering riboswitches: the past and the future.
Kavita et al. (2023)
2 more

6 mentions without citation

Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.
Troisi et al. (2023)
5 more