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

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Basic information

Entry
Database: PDB / ID: 31jo
TitlecryoEM structure of influenza B RNP-like particle with NPdel68
Components
  • Nucleoprotein
  • synthetic RNA
KeywordsVIRAL PROTEIN / RNA-protein complex / helical assembly / influenza B virus
Function / homologyRNA / RNA (> 10) / :
Function and homology information
Biological speciesInfluenza B virus
synthetic RNA (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsThirion, M. / Stelfox, A. / Chenavier, F. / Ruigrok, R. / Crepin, T. / Ballandras-Colas, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE11-0010-01 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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 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: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: synthetic RNA
E: synthetic RNA
F: synthetic RNA
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: synthetic RNA
K: synthetic RNA
L: synthetic RNA


Theoretical massNumber of molelcules
Total (without water)421,37812
Polymers421,37812
Non-polymers00
Water00
1
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: synthetic RNA
E: synthetic RNA
F: synthetic RNA
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: synthetic RNA
K: synthetic RNA
L: synthetic RNA
x 5


Theoretical massNumber of molelcules
Total (without water)2,106,88860
Polymers2,106,88860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 62938.391 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Protein deleted of the first 68 residues and fused to His-6 tag in C-ter.
Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: NP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5V913
#2: RNA chain
synthetic RNA


Mass: 7291.213 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic RNA (others)
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: RiboNucleoProtein (RNP)-like helical assembly / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 5 mM 2-Mercaptoethanol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
35 mM2-MercaptoethanolHOCH2CH2SH1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 38.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2EPUimage acquisition
4cryoSPARC4.7CTF correction
12cryoSPARC4.73D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 357020 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216485
ELECTRON MICROSCOPYf_angle_d0.61122469
ELECTRON MICROSCOPYf_dihedral_angle_d20.1863090
ELECTRON MICROSCOPYf_chiral_restr0.0382631
ELECTRON MICROSCOPYf_plane_restr0.0042616

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