› 6x5m

X-ray diffraction
2.5Å resolution

Crystal structure of a stabilized PAN ENE bimolecular triplex with a GC-clamped polyA tail, in complex with Fab-BL-3,6.

Released:
DOI: 10.2210/pdb6x5m/pdb
PDB entry 6x5m coloured by chain, front view.
PDB entry 6x5m coloured by chain, side view.
PDB entry 6x5m coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.
Swain M, Ageeli AA, Kasprzak WK, Li M, Miller JT, Sztuba-Solinska J, Schneekloth JS, Koirala D, Piccirili J, Fraboni AJ, Murelli RP, Wlodawer A, Shapiro BA, Baird N, Le Grice SFJ
Nucleic Acids Res 49 13179-13193 (2021)
PMID: 34871450

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-212935 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (4 distinct):
Light chain Fab BL-3 6 Chains: L, l
Molecule details ›
Chains: L, l
Length: 215 amino acids
Theoretical weight: 23.39 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Heavy chain Fab Bl-3 6 Chains: H, h
Molecule details ›
Chains: H, h
Length: 225 amino acids
Theoretical weight: 23.85 KDa
Source organism: Mus musculus
Expression system: Mus musculus
ggPAN RNA (39-MER) Chains: R, r
Molecule details ›
Chains: R, r
Length: 78 nucleotides
Theoretical weight: 24.76 KDa
ggcA9 RNA (12-MER) Chains: A, a
Molecule details ›
Chains: A, a
Length: 12 nucleotides
Theoretical weight: 3.91 KDa

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 43.128Å b: 76.26Å c: 110.664Å
α: 71.899° β: 88.591° γ: 86.579°
R-values:
R R work R free
0.209 0.207 0.279
Expression system: Mus musculus

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Citations

7 citation in other articles

LncRNA NEAT1 Potentiates SREBP2 Activity to Promote Inflammatory Macrophage Activation and Limit Hantaan Virus Propagation.
Yang et al. (2022)
6 more

1 mention without citation

Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.
Swain et al. (2021)