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- PDB-9vxy: Cryo-EM Structure of Nipah Virus Polymerase in complex with GL22 -

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Basic information

Entry
Database: PDB / ID: 9vxy
TitleCryo-EM Structure of Nipah Virus Polymerase in complex with GL22
Components
  • Phosphoprotein
  • RNA-directed RNA polymerase L
KeywordsREPLICATION / Polymerase / inhibitor / nipah virus / complex
Function / homology
Function and homology information


negative stranded viral RNA transcription / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase ...negative stranded viral RNA transcription / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / ATP binding
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase
Similarity search - Domain/homology
: / RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesHenipavirus nipahense
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsXue, L. / Gui, J. / Chang, T. / Pan, H. / Xiong, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400116 to L.X China
National Natural Science Foundation of China (NSFC)82341085 to X.X China
CitationJournal: Cell / Year: 2026
Title: Differential inhibition of Morbillivirus and Henipavirus polymerases by ERDRP-0519 and structure-guided inhibitor optimization.
Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / ...Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / Richard K Plemper / Xinwen Chen / Jun He / Rongjuan Pei / Peng Zhan / Xiaoli Xiong /
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 ...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.
History
DepositionJul 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,9458
Polymers571,1265
Non-polymers8193
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 257565.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q997F0, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase
#2: Protein
Phosphoprotein / Protein P


Mass: 78390.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Gene: P/V/C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IK91
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1ET4 / ~{N}-[4-[(2~{S})-2-[2-[4-[(2~{Z})-2-[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]iminoethanoyl]piperazin-1-yl]ethyl]piperidin-1-yl]sulfonylphenyl]-2-methyl-5-(trifluoromethyl)pyrazole-3-carboxamide


Mass: 687.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40F3N7O7S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM Structure of Nipah Virus Polymerase in complex with GL22
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Henipavirus nipahense
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4977110 / Symmetry type: POINT
RefinementHighest resolution: 2.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313044
ELECTRON MICROSCOPYf_angle_d0.58917609
ELECTRON MICROSCOPYf_dihedral_angle_d4.7921741
ELECTRON MICROSCOPYf_chiral_restr0.0442007
ELECTRON MICROSCOPYf_plane_restr0.0042233

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