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- EMDB-50805: Cryo-EM structure of the Nipah virus polymerase (L) bound to the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50805
TitleCryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)- Local map for L
Map data
Sample
  • Complex: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
KeywordsNipah virus L / Polymerase / Replicase / Transcriptase / VIRAL PROTEIN
Biological speciesHenipavirus nipahense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsBalikci E / Gunl F / Carrique L / Keown JR / Fodor E / Grimes JM
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-048922 United States
CitationJournal: EMBO J / Year: 2025
Title: Structure of the Nipah virus polymerase complex.
Authors: Esra Balıkçı / Franziska Günl / Loïc Carrique / Jeremy R Keown / Ervin Fodor / Jonathan M Grimes /
Abstract: Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral ...Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral polymerase complex, composed of the polymerase (L) and phosphoprotein (P), replicates and transcribes the viral RNA genome. Here, we describe structures of the Nipah virus L-P polymerase complex and the L-protein's Connecting Domain (CD). The cryo-electron microscopy L-P complex structure reveals the organization of the RNA-dependent RNA polymerase (RdRp) and polyribonucleotidyl transferase (PRNTase) domains of the L-protein, and shows how the P-protein, which forms a tetramer, interacts with the RdRp-domain of the L-protein. The crystal structure of the CD-domain alone reveals binding of three Mg ions. Modelling of this domain onto an AlphaFold 3 model of an RNA-L-P complex suggests a catalytic role for one Mg ion in mRNA capping. These findings offer insights into the structural details of the L-P polymerase complex and the molecular interactions between L-protein and P-protein, shedding light on the mechanisms of the replication machinery. This work will underpin efforts to develop antiviral drugs that target the polymerase complex of Nipah virus.
History
DepositionJun 26, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50805.png

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Map

FileDownload / File: emd_50805.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.914 Å		0.73 Å/pix.
x 512 pix.
= 373.914 Å		0.73 Å/pix.
x 512 pix.
= 373.914 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.3778465 - 0.48897696
Average (Standard dev.)-0.00009076722 (±0.008573499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.9136 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50805_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_50805_half_map_2.map
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Sample components

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Entire : Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

EntireName: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
Components
  • Complex: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

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Supramolecule #1: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

SupramoleculeName: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 570 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6748913
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.4.1) / Number images used: 299261
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: cryoSPARC (ver. V4.4.1)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL

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