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- EMDB-58449: cryoEM map of influenza B virus RNP-like particle with NPdel64 -

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Basic information

Entry
Database: EMDB / ID: EMD-58449
TitlecryoEM map of influenza B virus RNP-like particle with NPdel64
Map data
Sample
  • Complex: RiboNucleoProtein (RNP)-like helical assembly
    • Protein or peptide: Nucleoprotein
    • RNA: synthetic RNA
KeywordsRNA-protein complex / helical assembly / influenza B virus / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesInfluenza B virus (B/Memphis/13/2003) / synthetic RNA (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsThirion M / Stelfox AJ / Chenavier F / Ruigrok R / Crepin T / Ballandras-Colas A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE11-01 France
CitationJournal: PLoS Pathog / Year: 2026
Title: Nucleocapsid-like cryo-EM structure of influenza B virus.
Authors: Marie Thirion / Alice J Stelfox / Florian Chenavier / Héléna Chomat / Catherine Isel / Lily-Lorette Freslon / Eleftherios Zarkadas / Rob W H Ruigrok / Nadia Naffakh / Thibaut Crépin / ...Authors: Marie Thirion / Alice J Stelfox / Florian Chenavier / Héléna Chomat / Catherine Isel / Lily-Lorette Freslon / Eleftherios Zarkadas / Rob W H Ruigrok / Nadia Naffakh / Thibaut Crépin / Allison Ballandras-Colas /
Abstract: Influenza viruses belong to the Orthomyxoviridae family, they are categorized into four types: A, B, C, and D. Influenza B viruses co-circulate annually with influenza A strains during seasonal flu ...Influenza viruses belong to the Orthomyxoviridae family, they are categorized into four types: A, B, C, and D. Influenza B viruses co-circulate annually with influenza A strains during seasonal flu epidemics in humans, causing severe disease. The segmented RNA encapsidated by multiple copies of the nucleoprotein (NP) and attached to the heterotrimeric polymerase forms the central replicative unit called the viral ribonucleoprotein (vRNP). All influenza NP proteins share the same core domain folding, only NP of influenza B virus (B/NP) has an extended unfolded N-terminal tail of 70 amino-acids. This disordered N-terminal tail is required for nuclear localization of the protein, and may be involved in viral RNA transcription and replication regulation. In this study, we report that in absence of the extended N-terminal tail, the truncated NP maintains RNA binding ability and NP oligomeric state in vitro. We then reconstituted RNP-like particles by incubating truncated B/NP with synthetic RNA and we solved the cryo-EM structure at 4.1 Å resolution. Their morphology appears identical to native vRNPs extracted from viruses when observed by negative-stain electron microscopy. Overall, our results suggest that vRNPs from influenza virus type A, B and D share the same right-handed antiparallel helical conformation and that the B/NP N-terminal tail does not participate to the helical architecture stabilization once the vRNPs are assembled.
History
DepositionJun 9, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58449.png

Downloads & links

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Map

FileDownload / File: emd_58449.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.29 Å/pix.
x 200 pix.
= 458. Å		2.29 Å/pix.
x 200 pix.
= 458. Å		2.29 Å/pix.
x 200 pix.
= 458. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.95
Minimum - Maximum-3.1475487 - 6.015017
Average (Standard dev.)0.004910251 (±0.113902405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 458.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58449_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58449_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58449_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RiboNucleoProtein (RNP)-like helical assembly

EntireName: RiboNucleoProtein (RNP)-like helical assembly
Components
  • Complex: RiboNucleoProtein (RNP)-like helical assembly
    • Protein or peptide: Nucleoprotein
    • RNA: synthetic RNA

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Supramolecule #1: RiboNucleoProtein (RNP)-like helical assembly

SupramoleculeName: RiboNucleoProtein (RNP)-like helical assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Details: Nucleoprotein with His-6 tag fused in Cterm / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNMDIDGIN TGTIDKAPEE ITSGTSGTTR PIIRPATLAP PSNKRTRNPS PERATTISEA DVGRKTQKK QTPTEIKKSV YNMVVKLGEF YNQMMVKAGL NDDMERNLIQ NAHAVERILL A ATDDKKTE FQKKKNARDV KEGKEEIDHN KTGGTFYKMV RDDKTIYFSP ...String:
MSNMDIDGIN TGTIDKAPEE ITSGTSGTTR PIIRPATLAP PSNKRTRNPS PERATTISEA DVGRKTQKK QTPTEIKKSV YNMVVKLGEF YNQMMVKAGL NDDMERNLIQ NAHAVERILL A ATDDKKTE FQKKKNARDV KEGKEEIDHN KTGGTFYKMV RDDKTIYFSP IRVTFLKEEV KT MYKTTMG SDGFSGLNHI MIGHSQMNDV CFQRSKALKR VGLDPSLIST FAGSTLPRRS GAT GVAIKG GGTLVAEAIR FIGRAMADRG LLRDIKAKTA YEKILLNLKN KCSAPQQKAL VDQV IGSRN PGIADIEDLT LLARSMVVVR PSVASKVVLP ISIYAKIPQL GFNVEEYSMV GYEAM ALYN MATPVSILRV GDDAKDKSQL FFMSCFGAAY EDLRVLSALT GTEFKPRSAL KCKGFH VPA KEQVEGMGAA LMSIKLQFWA PMTRSGGNEV GGDGGSGQIS CSPVFAVERP IALSKQA VR RMLSMNIEGR DADVKGNLLK MMNDSMAKKT NGNAFIGKKM FQISDKNKTN PVEIPIKQ T IPNFFFGRDT AEDYDDLDYI NLEHHHHHH

UniProtKB: UNIPROTKB: Q5V913

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Macromolecule #2: synthetic RNA

MacromoleculeName: synthetic RNA / type: rna / ID: 2
Source (natural)Organism: synthetic RNA (others)
SequenceString:
UCUCUCUCUC UCUCUCUCUC UCUC

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClsodium chloride
5.0 mMHOCH2CH2SH2-Mercaptoethanol

Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 5 mM 2-Mercaptoethanol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 2053 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 297594
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7)
Details: Maximum likelyhood plus stochastic gradient descent (Punjani et al, Nat. Methods, 2017 https://doi.org/10.1038/nmeth.4169)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Details: Maximum likelyhood plus stochastic gradient descent (Punjani et al, Nat. Methods, 2017 https://doi.org/10.1038/nmeth.4169)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-31jo:
cryoEM structure of influenza B RNP-like particle with NPdel68

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