9OCF | pdb_00009ocf

2.73A cryo-EM structure of the Measles Virus L-P in complex with ERdRp-0519

• PDB DOI: https://doi.org/10.2210/pdb9OCF/pdb
• EM Map EMD-70313: EMDB EMDataResource

• Classification: VIRAL PROTEIN, TRANSFERASE
• Organism(s): Measles virus strain Edmonston-B
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-04-24 Released: 2025-09-03 
• Deposition Author(s): Liu, B., Wang, D., Yang, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of measles virus polymerase inhibition by nonnucleoside inhibitor ERDRP-0519.

Wang, D., Bu, F., Yang, G., Liu, B.

(2025) Nat Commun 16: 9061-9061

• PubMed: 41083444 
• DOI: https://doi.org/10.1038/s41467-025-64128-0
• Primary Citation of Related Structures:  
  9OCE, 9OCF


• PubMed Abstract: 
  

  ERDRP-0519 is a potent nonnucleoside inhibitor active against measles virus (MeV) and other Morbilliviruses. Here we report cryo-EM structures of the compound bound to MeV polymerase complexes at 2.73 Å and 2.48 Å resolution, revealing a unique binding pocket in the RdRp palm subdomain that overlaps the catalytic GDN motif. These findings clarify the basis of resistance mutations, including W671, and provide a foundation for designing next-generation Paramyxovirus antivirals.

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Organizational Affiliation: 
• Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.
Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.
Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 464.79 kDa 
• Atom Count: 12,449 
• Modeled Residue Count: 1,558 
• Deposited Residue Count: 4,219 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,183	Measles virus strain Edmonston-B	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1 (PDB Primary Data), 2.1.1.375 (UniProt)
UniProt
Find proteins for P12576 (Measles virus (strain Edmonston)) Explore P12576  Go to UniProtKB:  P12576

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	B, C, D, E	509	Measles virus strain Edmonston-B	Mutation(s): 0  Gene Names: P/V
UniProt
Find proteins for P03422 (Measles virus (strain Edmonston)) Explore P03422  Go to UniProtKB:  P03422

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EF9 (Subject of Investigation/LOI)	F [auth A]	2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide C23 H30 F3 N5 O4 S JVZHTUQIMBYDSX-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Liu, B., Wang, D., Yang, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Data collection, Database references
• Version 1.2: 2025-10-29
  Changes: Data collection, Database references