6X5M | pdb_00006x5m

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

• PDB DOI: https://doi.org/10.2210/pdb6X5M/pdb
• NAKB: 6X5M

• Classification: Immune System/RNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2020-05-26 Released: 2020-06-24 
• Deposition Author(s): Swain, M., Li, M., Wlodawer, A., Le Grice, S.F.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.

Swain, M., Ageeli, A.A., Kasprzak, W.K., Li, M., Miller, J.T., Sztuba-Solinska, J., Schneekloth, J.S., Koirala, D., Piccirili, J., Fraboni, A.J., Murelli, R.P., Wlodawer, A., Shapiro, B.A., Baird, N., Le Grice, S.F.J.

(2021) Nucleic Acids Res 49: 13179-13193

• PubMed: 34871450 
• DOI: https://doi.org/10.1093/nar/gkab1170
• Primary Citation Related Structures: 
  6X5M, 6X5N


• PubMed Abstract: 
  

  Cellular and virus-coded long non-coding (lnc) RNAs support multiple roles related to biological and pathological processes. Several lncRNAs sequester their 3' termini to evade cellular degradation machinery, thereby supporting disease progression. An intramolecular triplex involving the lncRNA 3' terminus, the element for nuclear expression (ENE), stabilizes RNA transcripts and promotes persistent function. Therefore, such ENE triplexes, as presented here in Kaposi's sarcoma-associated herpesvirus (KSHV) polyadenylated nuclear (PAN) lncRNA, represent targets for therapeutic development. Towards identifying novel ligands targeting the PAN ENE triplex, we screened a library of immobilized small molecules and identified several triplex-binding chemotypes, the tightest of which exhibits micromolar binding affinity. Combined biophysical, biochemical, and computational strategies localized ligand binding to a platform created near a dinucleotide bulge at the base of the triplex. Crystal structures of apo (3.3 Å) and ligand-soaked (2.5 Å) ENE triplexes, which include a stabilizing basal duplex, indicate significant local structural rearrangements within this dinucleotide bulge. MD simulations and a modified nucleoside analog interference technique corroborate the role of the bulge and the base of the triplex in ligand binding. Together with recently discovered small molecules that reduce nuclear MALAT1 lncRNA levels by engaging its ENE triplex, our data supports the potential of targeting RNA triplexes with small molecules.

---

Organizational Affiliation: 
• Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104, USA.
Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia.
Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, 11210, USA.
PhD Program in Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA.
PhD Program in Biochemistry, The Graduate Center, City University of New York, New York, NY 10016, USA.
RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 152.04 kDa 
• Atom Count: 8,881 
• Modeled Residue Count: 982 
• Deposited Residue Count: 1,060 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain Fab BL-3 6	A [auth l], D [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain Fab Bl-3 6	B [auth h], C [auth H]	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
ggPAN RNA (39-MER)	E [auth R], G [auth r]	78	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
ggcA9 RNA (12-MER)	F [auth A], H [auth a]	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	I [auth l], J [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.279 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.128	α = 71.899
b = 76.26	β = 88.591
c = 110.664	γ = 86.579

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Swain, M., Li, M., Wlodawer, A., Le Grice, S.F.J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 2.0: 2021-02-03
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2021-12-22
  Changes: Advisory, Database references
• Version 2.2: 2021-12-29
  Changes: Database references
• Version 2.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.4: 2024-10-23
  Changes: Structure summary