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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: To Be Published
Title: Nucleocapsid-like cryoEM structure of influenza B virus
Authors: Thirion, M. / Stelfox, A. / Chenavier, F. / Chomat, H. / Isel, C. / Freslon, L.L. / Zarkadas, E. / Ruigrok, R. / Naffakh, N. / Crepin, T. / Ballandras-Colas, A.
History
DepositionJun 9, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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