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- EMDB-52031: TiLV-NP tetramer (pseudo-C4) (local refinement around 2 TiLV-NPs) -

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Basic information

Entry
Database: EMDB / ID: EMD-52031
TitleTiLV-NP tetramer (pseudo-C4) (local refinement around 2 TiLV-NPs)
Map datasharpened
Sample
  • Complex: TiLV-NP bound to the 40-mer vRNA loop
    • Protein or peptide: Tilapia Lake Virus nucleoprotein (segment 4)
    • RNA: 40-mer vRNA loop
    • RNA: 40-mer vRNA loop
KeywordsViral protein / nucleoprotein / oligomer / RNA BINDING PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesTilapia lake virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsArragain B / Cusack S
Funding support France, 1 items
OrganizationGrant numberCountry
Other government France
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structure of the tilapia lake virus nucleoprotein bound to RNA.
Authors: Benoît Arragain / Martin Pelosse / Karine Huard / Stephen Cusack /
Abstract: Tilapia Lake virus (TiLV) belongs to the Amnoonviridae family within the Articulavirales order of segmented negative-strand RNA viruses and is highly diverged from more familiar orthomyxoviruses, ...Tilapia Lake virus (TiLV) belongs to the Amnoonviridae family within the Articulavirales order of segmented negative-strand RNA viruses and is highly diverged from more familiar orthomyxoviruses, such as influenza. The viral nucleoprotein (NP), a key component of the replication machinery, packages the viral genome into protective ribonucleoprotein particles. Here we describe the electron cryo-microscopy (cryo-EM) structure of TiLV-NP bound to RNA within in vitro reconstituted, small ring-like, pseudo-symmetrical oligomers. Although TiLV-NP is considerably smaller than its influenza counterpart and unrelated in sequence, it maintains the same topology and domain organisation. This comprises a head and body domain between which is a positively charged groove, where single-stranded RNA binds. In addition, an oligomerisation loop inserts into a hydrophobic pocket in the neighbouring NP, the flexible hinges of which allow variable orientation of adjacent NPs. Focused cryo-EM maps unambiguously define the 5' to 3' direction of the bound RNA, confirmed by double stranded, A-form RNA regions that extrude out from some of the NP-NP interfaces. This is the first fully resolved description of how single-stranded and stem-loop RNA binds to an articulaviral NP assembly. Superposition with orthomyxoviral NPs suggest that the mode of RNA binding is likely similar across the Articulavirales order.
History
DepositionNov 8, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52031.png

Downloads & links

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Map

FileDownload / File: emd_52031.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 340 pix.
= 279.48 Å		0.82 Å/pix.
x 340 pix.
= 279.48 Å		0.82 Å/pix.
x 340 pix.
= 279.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.45368642 - 0.6860477
Average (Standard dev.)-0.00013855916 (±0.009414721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 279.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52031_msk_1.map
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Additional map: unsharpened

Fileemd_52031_additional_1.map
Annotationunsharpened
Projections & Slices
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Half map: #1

Fileemd_52031_half_map_1.map
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Half map: #2

Fileemd_52031_half_map_2.map
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Sample components

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Entire : TiLV-NP bound to the 40-mer vRNA loop

EntireName: TiLV-NP bound to the 40-mer vRNA loop
Components
  • Complex: TiLV-NP bound to the 40-mer vRNA loop
    • Protein or peptide: Tilapia Lake Virus nucleoprotein (segment 4)
    • RNA: 40-mer vRNA loop
    • RNA: 40-mer vRNA loop

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Supramolecule #1: TiLV-NP bound to the 40-mer vRNA loop

SupramoleculeName: TiLV-NP bound to the 40-mer vRNA loop / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tilapia lake virus

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Macromolecule #1: Tilapia Lake Virus nucleoprotein (segment 4)

MacromoleculeName: Tilapia Lake Virus nucleoprotein (segment 4) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tilapia lake virus
Molecular weightTheoretical: 38.387129 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVRTTKTSMA AASTVAPEVA MDEGSPSTSQ AQVELPRNLE VFNEACGHVF GSSFNREDNS VISDAAAFLF KMHTHSLDGQ EAKVLRASE KKRERENAKK SRKAPEAGMR VGRSLILTSR WTEYCATCVP ALGSKMKVIK ASGDAAMIQM MKDHNSLLRV C VRIEVWKA ...String:
MVRTTKTSMA AASTVAPEVA MDEGSPSTSQ AQVELPRNLE VFNEACGHVF GSSFNREDNS VISDAAAFLF KMHTHSLDGQ EAKVLRASE KKRERENAKK SRKAPEAGMR VGRSLILTSR WTEYCATCVP ALGSKMKVIK ASGDAAMIQM MKDHNSLLRV C VRIEVWKA RYVSLVALDE RIQTLEDAQW FPYLSGDSYR ACPGLVGGYF AKKAAAGERG KNYKKLNQTA IIPPPRFLII GH RLQIGDQ VTLRELLASI AWGLCDGVLA ECWSPSQGDG SIGVVVGLPL QATGSCFLVV ASHGLSAIAD SRIEGTGNTN LLE ECIAIQ KQDGVIKCKR SGKSLYHCLK ETAGAVGR

UniProtKB: Uncharacterized protein

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Macromolecule #2: 40-mer vRNA loop

MacromoleculeName: 40-mer vRNA loop / type: rna / ID: 2
Details: The RNA sequence (40-mer vRNA loop) is 5' - pGCA AAU CUU UCU CAC GUC CUG ACU UGU GAG UAA AAU UUG G - 3'. Due to the inability to precisely define bases, the exact nucleotide register remains ...Details: The RNA sequence (40-mer vRNA loop) is 5' - pGCA AAU CUU UCU CAC GUC CUG ACU UGU GAG UAA AAU UUG G - 3'. Due to the inability to precisely define bases, the exact nucleotide register remains elusive. Thus, in the modelling, generic purines (P5P) and generic pyrimidines (Y5P) were assigned based on apparent base size.
Number of copies: 1
Source (natural)Organism: Tilapia lake virus
Molecular weightTheoretical: 2.982934 KDa
SequenceString:
(P5P)(P5P)(P5P)(P5P)(P5P)(Y5P)(Y5P)(P5P)(P5P)(Y5P)

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Macromolecule #3: 40-mer vRNA loop

MacromoleculeName: 40-mer vRNA loop / type: rna / ID: 3
Details: The RNA sequence (40-mer vRNA loop) is 5' - pGCA AAU CUU UCU CAC GUC CUG ACU UGU GAG UAA AAU UUG G - 3'. Due to the inability to precisely define bases, the exact nucleotide register remains ...Details: The RNA sequence (40-mer vRNA loop) is 5' - pGCA AAU CUU UCU CAC GUC CUG ACU UGU GAG UAA AAU UUG G - 3'. Due to the inability to precisely define bases, the exact nucleotide register remains elusive. Thus, in the modelling, generic purines (P5P) and generic pyrimidines (Y5P) were assigned based on apparent base size.
Number of copies: 1
Source (natural)Organism: Tilapia lake virus
Molecular weightTheoretical: 5.85879 KDa
SequenceString:
(Y5P)(Y5P)(Y5P)(Y5P)(Y5P)(P5P)(Y5P)(P5P)(P5P)(P5P) (P5P)(P5P)(P5P)(P5P)(P5P)(Y5P) (Y5P)(Y5P)(P5P) (Y5P)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 97514
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9hbv:
TiLV-NP tetramer (pseudo-C4) (local refinement around 2 TiLV-NPs)

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