9VUM | pdb_00009vum

Cryo-EM structure of the Nipah virus RNA-dependent RNA polymerase complex bound to allosteric inhibitor ERDRP-0519


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural insights into measles virus RNA synthesis regulation and pan-paramyxoviral polymerase inhibition by ERDRP-0519.

Du, T.Wang, J.Yang, C.Xue, R.Chen, Y.Jie, K.Zhang, X.Zhang, L.Song, G.Zhang, Q.Wu, S.Ru, H.

(2026) Proc Natl Acad Sci U S A 123: e2522978123-e2522978123

  • DOI: https://doi.org/10.1073/pnas.2522978123
  • Primary Citation Related Structures: 
    9VUI, 9VUJ, 9VUK, 9VUL, 9VUM

  • PubMed Abstract: 

    Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent RNA polymerase (RdRP) complex for transcription and replication. In measles virus (MeV), the nonstructural protein C has long been implicated in regulating RNA synthesis, yet its precise role remains unclear. Here, we show that the MeV C protein directly associates with the RdRP complex. Using cryoelectron microscopy, we determined atomic-resolution structures of the MeV polymerase with and without C, revealing that C binding stabilizes the C-terminal region of L and locks the complex into a replication-competent elongation state. Biochemical data further show that C promotes N protein recruitment, enhancing polymerase processivity through facilitating encapsidation during replication. Additionally, we also resolved high-resolution structures of MeV and Nipah virus (NiV) polymerases bound to ERDRP-0519, an orally available morbillivirus inhibitor. Unexpectedly, the compound occupies an allosteric pocket within the RdRp domain rather than the previously predicted PRNTase domain, overlapping conserved resistance sites. This binding induces conformational changes in palm subdomain, blocking RNA template and nucleotide engagement, thereby halting RNA synthesis. These findings uncover distinct regulatory and inhibitory mechanisms in paramyxovirus polymerases and provide a structural framework for the rational design of broad-spectrum antivirals targeting MeV, NiV, and potentially other clinically relevant nsNSVs.


  • Organizational Affiliation
    • Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Molecular Cancer Biology, Zhejiang University, Hangzhou 310058, China.

Macromolecule Content 

  • Total Structure Weight: 500.47 kDa 
  • Atom Count: 12,867 
  • Modeled Residue Count: 1,599 
  • Deposited Residue Count: 4,456 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase LA [auth L]1,904Escherichia coli K-12Henipavirus nipahense
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994
EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.375 (PDB Primary Data)
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q997F0 (Nipah virus)
Explore Q997F0 
Go to UniProtKB:  Q997F0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ997F0P0AEX9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,PhosphoproteinB [auth A],
C [auth B],
D [auth C],
E [auth D]
638Escherichia coli K-12Henipavirus nipahense
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994P/V/C
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9IK91 (Nipah virus)
Explore Q9IK91 
Go to UniProtKB:  Q9IK91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q9IK91
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371344

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release