7U4A | pdb_00007u4a

Crystal Structure of Zika virus xrRNA1 mutant

• PDB DOI: https://doi.org/10.2210/pdb7U4A/pdb
• NAKB: 7U4A

• Classification: RNA
• Organism(s): Zika virus
• Mutation(s): No 


• Deposited: 2022-02-28 Released: 2023-09-06 
• Deposition Author(s): Thompson, R.D., Carbaugh, D.L., Nielsen, J.R., Witt, C., Meganck, R.M., Rangadurai, A., Zhao, B., Bonin, J.P., Nathan, N.T., Marzluff, W.F., Frank, A.T., Lazear, H.M., Zhang, Q.
• Funding Organization(s): University of North Carolina at Chapel Hill

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Lifetime of ground conformational state determines the activity of structured RNA.

Thompson, R.D., Carbaugh, D.L., Nielsen, J.R., Witt, C.M., Faison, E.M., Meganck, R.M., Rangadurai, A., Zhao, B., Bonin, J.P., Nicely, N.I., Marzluff, W.F., Frank, A.T., Lazear, H.M., Zhang, Q.

(2025) Nat Chem Biol 

• PubMed: 39939412 
• DOI: https://doi.org/10.1038/s41589-025-01843-1
• Primary Citation of Related Structures:  
  7U4A


• PubMed Abstract: 
  

  Biomolecules continually sample alternative conformations. Consequently, even the most energetically favored ground conformational state has a finite lifetime. Here, we show that, in addition to the three-dimensional (3D) structure, the lifetime of a ground conformational state determines its biological activity. Using hydrogen-deuterium exchange nuclear magnetic resonance spectroscopy, we found that Zika virus exoribonuclease-resistant RNA (xrRNA) encodes a ground conformational state with a lifetime that is ~10 ⁵ -10 ⁷ longer than that of canonical base pairs. Mutations that shorten the apparent lifetime of the ground state without affecting its 3D structure decreased exoribonuclease resistance in vitro and impaired virus replication in cells. Additionally, we observed this exceptionally long-lived ground state in xrRNAs from diverse infectious mosquito-borne flaviviruses. These results demonstrate the biological importance of the lifetime of a preorganized ground state and further suggest that elucidating the lifetimes of dominant 3D structures of biomolecules may be crucial for understanding their behaviors and functions.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Biophysics and Chemistry, University of Michigan, Ann Arbor, MI, USA.
Department of Biochemistry, Duke University, Durham, NC, USA.
NanoVation Therapeutics, Vancouver, British Columbia, Canada.
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Biophysics and Chemistry, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Arrakis Therapeutics, Waltham, MA, USA. [e-mail].
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].
RNA Discovery Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.35 kDa 
• Atom Count: 1,503 
• Modeled Residue Count: 70 
• Deposited Residue Count: 72 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (70-MER)	A	72	Zika virus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.421	α = 90
b = 39.137	β = 94.339
c = 66.583	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Thompson, R.D., Carbaugh, D.L., Nielsen, J.R., Witt, C., Meganck, R.M., Rangadurai, A., Zhao, B., Bonin, J.P., Nathan, N.T., Marzluff, W.F., Frank, A.T., Lazear, H.M., Zhang, Q.

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Funding Organization	Location	Grant Number
University of North Carolina at Chapel Hill	United States	--

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references, Structure summary