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- PDB-9v48: Coupling of polymerase-nucleoprotein-RNA in an influenza virus mi... -

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Basic information

Entry
Database: PDB / ID: 9v48
TitleCoupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex
Components
  • Nucleoprotein
  • RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*GP*UP*UP*UP*UP*UP*UP*AP*U)-3')
  • RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
KeywordsVIRAL PROTEIN/RNA / Influenza virus / ribonucleoprotein complex / polymerase / cryo-EM / 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 A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.75 Å
AuthorsKang, H. / Yang, Y. / Liu, Y. / Li, M. / Zhang, L. / Lin, Y. / Rao, Z. / Lou, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Coupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex.
Authors: Huiling Kang / Yunxiang Yang / Yixiao Liu / Mingyu Li / Lejin Zhang / Yuqi Lin / Leander Witte / Kuang-Yu Chen / Wenya Song / Zhili Xu / Xiaojing He / Luke W Guddat / Yu Guo / Liming Yan / ...Authors: Huiling Kang / Yunxiang Yang / Yixiao Liu / Mingyu Li / Lejin Zhang / Yuqi Lin / Leander Witte / Kuang-Yu Chen / Wenya Song / Zhili Xu / Xiaojing He / Luke W Guddat / Yu Guo / Liming Yan / Yan Gao / Ervin Fodor / Zihe Rao / Zhiyong Lou /
Abstract: Influenza virus ribonucleoprotein complexes (RNPs), composed of the polymerase complex (FluPol), nucleoprotein (NP), and RNA, are essential for replication and transcription. We report atomic- ...Influenza virus ribonucleoprotein complexes (RNPs), composed of the polymerase complex (FluPol), nucleoprotein (NP), and RNA, are essential for replication and transcription. We report atomic-resolution cryo-EM structures of mini-vRNPs in two states: FluPol located inside (State-In) or at the outer rim (State-Out) of the NP-RNA ring. In both states, the 5' and 3' termini of vRNA are bound to FluPol as previously reported. One NP (NP-0) contacts PA/PB1 of FluPol and binds the distal double-stranded vRNA promoter, with its D72-K90 loop inserting into the RNA fork; separated strands occupy NP-0 RNA-binding grooves. Grooves from other NPs form a continuous RNA-protective path, consistent with negative-strand RNA virus mechanisms. In State-In, interfaces for FluPol dimerization or Pol II interaction are blocked, but fully exposed in State-Out. These structures reveal detailed FluPol-NP-RNA coupling and suggest a conformational shift in RNPs during the viral life cycle.
History
DepositionMay 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Nucleoprotein
E: RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
F: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*GP*UP*UP*UP*UP*UP*UP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)68,8423
Polymers68,8423
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 56172.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2))
Gene: NP / Production host: Homo sapiens (human) / References: UniProt: Q9WLG4
#2: RNA chain RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')


Mass: 4948.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2))
Production host: Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*GP*UP*UP*UP*UP*UP*UP*AP*U)-3')


Mass: 7720.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2))
Production host: Homo sapiens (human)
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: NP-0_RNA_State In / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265200 / Symmetry type: POINT

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