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- PDB-9bwv: Structure of influenza D RNP, 4xNP local resconstruction -

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Basic information

Entry
Database: PDB / ID: 9bwv
TitleStructure of influenza D RNP, 4xNP local resconstruction
Components
  • FluD-NS vRNA
  • Nucleoprotein
KeywordsVIRAL PROTEIN/RNA / Influenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza D virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsPeng, R. / Chang, Y.-W.
Funding support United States, 1items
OrganizationGrant numberCountry
David and Lucile Packard Foundation2019-69645 United States
CitationJournal: Science / Year: 2025
Title: Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis.
Authors: Ruchao Peng / Xin Xu / Binod Nepal / Yikang Gong / Fenglin Li / Max B Ferretti / Mingyang Zhou / Kristen W Lynch / George M Burslem / Sandhya Kortagere / Ronen Marmorstein / Yi-Wei Chang /
Abstract: Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo-electron microscopy single-particle analysis and cryo- ...Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo-electron microscopy single-particle analysis and cryo-electron tomography, we define the influenza RNP as a right-handed, antiparallel double helix with the viral RNA encapsidated in the minor groove. Individual nucleoprotein subunits are connected by a flexible tail loop that inserts into a conserved pocket in its neighbor. We visualize the viral polymerase in RNP at different functional states, revealing how it accesses the RNA template while maintaining the double-helical architecture of RNP by strand sliding. Targeting the tail loop binding interface, we identify lead compounds as potential anti-influenza inhibitors. These findings elucidate the molecular determinants underpinning influenza virus replication and highlight a promising target for antiviral development.
History
DepositionMay 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Revision 2.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Data updated
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
C: Nucleoprotein
E: Nucleoprotein
H: Nucleoprotein
B: FluD-NS vRNA
D: FluD-NS vRNA
F: FluD-NS vRNA
G: FluD-NS vRNA


Theoretical massNumber of molelcules
Total (without water)269,6308
Polymers269,6308
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Nucleoprotein


Mass: 61329.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus / Gene: NP / Production host: Homo sapiens (human) / References: UniProt: K9LG94
#2: RNA chain
FluD-NS vRNA


Mass: 6078.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus / Production host: Homo sapiens (human)
Has protein modificationN
Sequence detailsSample RNA sequence is ...Sample RNA sequence is AGCAGUAGCAAGGGGUUUUUUCAUACUAAAGAACGAAUACAUUCUUUUAACAUUGAAAUUGUUCUCGAAACUGACUUGAUUUCAUCCAAAGCGGCCCUCAUAUCCUGGUUAGUCAAAGAGUUCACCAUCGCUACUCCCAGCUUGGAUUUCAACCUUAUCAAUGACACCAAGCAACUCCUGAACCUCUCCAGUAGUUGCGCCUUCUCUUCUCCAGAAGGGAUCUGUUUCACAUCCAGAUUUGUAUCGUCUGAUUUCAUCUCUAGAUUCCGCAUCAACGGCAACAACAAGUCCACUUCUCCAAAUUCUGAGUAUCUUUCGUACUGACUUCUCUGGGUCAUCUCCUCUACGGAAAUUCUUAAGGCAGUAAGCUGGUUUCUCAGUGUUUCUGCAAAAGAGCACAAUGAUUUCUCCCAUGUCGGUCACUAAUAGUUCAGCAGUUUUUACAAAGCAAUUGCAGUUCCGAUAUUUUACUCCAAAGACUUCUCCUUGUCUUAUGAGCUUUGGCUCAUACAGAGUGUCAAUGGUACAUGGGCUUAGAUAGAAAGGGUUUCCUCCUAAGGGAUAGAUAAUGUUCUUCCCCAAUUCAACAGCAUGAGUCUCCUCUGGUUUUCUUAAGGCAGCAAUAGUAGUGAAUCCUAGAAUUUCUCUACCUUCAGCCACUGCAUCUUCCCAAGUUCUCGGUUCAUAAACCUGUUCGACUCUCAGUGAAUUCUCAGCAGACUUUCUCAUUUUCUCGAAAGUCAUUAACCCAGAGGAAUCCAUCCAGCUGGCUGCGCCCAAUGCCAAUUCGGAGAUUGCUGCUCUGAUAUUUGUUGUGUUCACUGACUUAUUUUCAGACAUAUUGAAAUUGUACACCCCUGCUUAUGCU

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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: influenza D virus RNP complex / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Influenza D virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 1x PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4particle selection
2EPU2.13image acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.5model fitting
9PHENIX1.19model refinement
10RELION3.1initial Euler assignment
11RELION5final Euler assignment
12RELION3.1classification
13RELION53D reconstructionDynaMight
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2000000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237636 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross correlation coefficient
Atomic model buildingPDB-ID: 5N2U

5n2u


Pdb chain-ID: A / Accession code: 5N2U / Source name: PDB / Type: experimental model

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