9OCE | pdb_00009oce

2.48A cryo-EM structure of the Measles Virus L-P-C in complex with ERdRp-0519

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 
    • Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,183Measles virus strain Edmonston-BMutation(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)
UniProt
Find proteins for P12576 (Measles virus (strain Edmonston))
Explore P12576 
Go to UniProtKB:  P12576
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12576
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoprotein
B, C, D, E
509Measles virus strain Edmonston-BMutation(s): 0 
Gene Names: P/V
UniProt
Find proteins for P03422 (Measles virus (strain Edmonston))
Explore P03422 
Go to UniProtKB:  P03422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03422
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein C
F, G
186Measles virus strain Edmonston-BMutation(s): 0 
Gene Names: C, P
UniProt
Find proteins for P03424 (Measles virus (strain Edmonston))
Explore P03424 
Go to UniProtKB:  P03424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03424
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EF9 (Subject of Investigation/LOI)
Query on A1EF9
Download Ideal Coordinates CCD File 
H [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: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • 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