9VXV | pdb_00009vxv

Cryo-EM Structure of Nipah Virus Polymerase in complex with ERDRP-0519

PDB DOI: https://doi.org/10.2210/pdb9VXV/pdb
EM Map EMD-65442: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Henipavirus nipahense
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-07-20 Released: 2026-04-29
Deposition Author(s): Xue, L., Gui, J., Chang, T., Pan, H., Xiong, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Differential inhibition of Morbillivirus and Henipavirus polymerases by ERDRP-0519 and structure-guided inhibitor optimization.

Xue, L., Gui, J., Gao, S., Gao, X., Chang, T., Pan, H., Tang, J., Zhang, M., Li, Z., Zou, B., Zhao, H., Wang, L., Li, M., Rong, L., Plemper, R.K., Chen, X., He, J., Pei, R., Zhan, P., Xiong, X.

(2026) Cell

PubMed: 42061399 Search on PubMed
DOI: https://doi.org/10.1016/j.cell.2026.04.011
Primary Citation Related Structures:
21XO, 9VXV, 9VXX, 9VXY, 9VXZ, 9VY0, 9VY1

PubMed Abstract:
ERDRP-0519 is a non-nucleoside polymerase inhibitor developed against measles virus (MeV) of the Morbillivirus genus. Here, we show that ERDRP-0519 also cross-inhibits Nipah virus (NiV) of the Henipavirus genus with reduced potency. ERDRP-0519 binds to a shared pocket within the RNA-dependent RNA polymerase (RdRp) palm domains of MeV, peste des petits ruminants virus (PPRV), and NiV polymerases. ERDRP-0519 forms more extensive interactions with Morbillivirus polymerases, whereas binding to NiV polymerase requires substantial RdRp motif rearrangements, likely incurring an energetic cost and resulting in reduced affinity. ERDRP-0519 binding impedes RNA synthesis by sterically blocking RNA and nucleotide binding. Guided by these insights, we designed GL22 and G671, ERDRP-0519 derivatives with extended moieties that engage additional cross-domain RdRp contacts in the NiV polymerase. These derivatives exert more extensive steric hindrance to RNA and nucleotide binding, enhancing biochemical inhibition potency. These findings elucidate the molecular mechanism of ERDRP-0519 action and guide structure-based inhibitor design.

Organizational Affiliation

State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China.

Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.

State Key Laboratory of Virology and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.

Guangzhou National Laboratory, Guangzhou 510005, China.

State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 511436, China; Guangzhou National Laboratory, Guangzhou 510005, China.

Departments of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA.

Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.

Guangzhou National Laboratory, Guangzhou 510005, China. Electronic address: chen_xinwen@gzlab.ac.cn.

State Key Laboratory of Virology and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. Electronic address: rongjuan_pei@wh.iov.cn.

Macromolecule Content

Total Structure Weight: 571.79 kDa
Atom Count: 13,295
Modeled Residue Count: 1,651
Deposited Residue Count: 5,080
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,244	Henipavirus nipahense	Mutation(s): 0 EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.375 (PDB Primary Data)
UniProt
Find proteins for Q997F0 (Nipah virus) Explore Q997F0 Go to UniProtKB: Q997F0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q997F0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	B, C, D, E	709	Henipavirus nipahense	Mutation(s): 0 Gene Names: P/V/C
UniProt
Find proteins for Q9IK91 (Nipah virus) Explore Q9IK91 Go to UniProtKB: Q9IK91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9IK91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EF9 (Subject of Investigation/LOI) Query on A1EF9 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]