8UTG

An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome

• PDB DOI: https://doi.org/10.2210/pdb8UTG/pdb
• NAKB: 8UTG

• Classification: RNA
• Organism(s): West Nile virus strain NY-99
• Mutation(s): No 


• Deposited: 2023-10-31 Released: 2024-06-19 
• Deposition Author(s): Terrell, J.R., Le, T.T., Wilson, W.D., Siemer, J.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.243 
• R-Value Work: 0.194 
• R-Value Observed: 0.199 

Literature

Structure of an RNA G-Quadruplex from the West Nile Virus Genome

Terrell, J.R., Le, T.T., Paul, A., Poon, G.M.K., Brinton, M.A., Germann, M.W., Wilson, W.D., Siemer, J.L.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry, native gel electrophoresis

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.83 kDa 
• Atom Count: 935 
• Modelled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')	A, B	21	West Nile virus strain NY-99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	D [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NH4 (Subject of Investigation/LOI)	C [auth A], E [auth A], G [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.243 
• R-Value Work: 0.194 
• R-Value Observed: 0.199 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.805	α = 90
b = 33.805	β = 90
c = 163.376	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Terrell, J.R., Le, T.T., Wilson, W.D., Siemer, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U19AI171403-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749
National Science Foundation (NSF, United States)	United States	MCB2028902
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL155178

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release