8PFK | pdb_00008pfk

RNA structure with 1-methylpseudouridine, C2 space group

• PDB DOI: https://doi.org/10.2210/pdb8PFK/pdb
• NAKB: 8PFK

• 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: 1.32 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

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 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.
Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.
Biosynth Limited, Compton, Berkshire, RG20 6NE, United Kingdom.
Institut für Nanostruktur und Festkörperphysik, Universität Hamburg, 22761, Hamburg, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.91 kDa 
• Atom Count: 353 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (12-mer)	A	12	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.295	α = 90
b = 34.777	β = 128.07
c = 31.685	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	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
• Version 1.3: 2024-11-06
  Changes: Structure summary
• Version 1.4: 2025-02-19
  Changes: Derived calculations