8PFQ

RNA structure with 1-methylpseudoridine, P1 space group

• PDB DOI: https://doi.org/10.2210/pdb8PFQ/pdb
• NAKB: 8PFQ

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-06-16 Released: 2024-01-31 
• Deposition Author(s): Spingler, B., McAuley, K., Nievergelt, P., Thorn, A.
• Funding Organization(s): University of Zurich, Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.175 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

RNA oligomers at atomic resolution containing 1-methylpseudouridine, an essential building block of mRNA vaccines.

Nievergelt, P., Berliat, F., McAuley, K.E., Dorgan, C.R., van Well, R.M., Thorn, A., Spingler, B.

(2024) ChemMedChem 19: e202300600-e202300600

• PubMed: 38235959 
• DOI: https://doi.org/10.1002/cmdc.202300600
• Primary Citation of Related Structures:  
  8PFK, 8PFQ


• PubMed Abstract: 
  

  All widely used mRNA vaccines against COVID-19 contain in their sequence 1-methylpseudouridine (m1Ψ) instead of uridine. In this publication, we report two high resolution crystal structures (at up to 1.01 and 1.32 Å, respectively) of one such double-stranded 12-mer RNA sequence crystallized in two crystal forms. The structures are compared with similar structures which do not contain this modification. Additionally, the X-ray structure of 1-methyl-pseudouridine itself was determined.

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Organizational Affiliation: 

Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.8 kDa 
• Atom Count: 682 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Chains: A,B	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.175 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.763	α = 62.59
b = 27.037	β = 63.8
c = 29.141	γ = 88.7

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Spingler, B., McAuley, K., Nievergelt, P., Thorn, A.

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Funding Organization	Location	Grant Number
University of Zurich	Switzerland	--
Swiss National Science Foundation	Switzerland	206021_164018

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-04-24
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Database references