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- EMDB-64770: Coupling of polymerase-nucleoprotein-RNA in an influenza virus mi... -

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Basic information

Entry
Database: EMDB / ID: EMD-64770
TitleCoupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex
Map data
Sample
  • Complex: NP-0_RNA_State In
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
    • RNA: 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')
KeywordsInfluenza virus / ribonucleoprotein complex / polymerase / cryo-EM / VIRAL PROTEIN/RNA / 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
Biological speciesInfluenza A virus (A/Victoria/3/1975(H3N2))
Methodsingle 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 support1 items
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, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64770.png

Downloads & links

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Map

FileDownload / File: emd_64770.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.96519923 - 2.439974
Average (Standard dev.)0.0009134197 (±0.028352777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64770_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: #1

Fileemd_64770_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : NP-0_RNA_State In

EntireName: NP-0_RNA_State In
Components
  • Complex: NP-0_RNA_State In
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
    • RNA: 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')

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Supramolecule #1: NP-0_RNA_State In

SupramoleculeName: NP-0_RNA_State In / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 56.172574 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASQGTKRSY EQMETDGERQ NATEIRASVG KMINGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNRYLE EHPSAGKDP KKTGGPIYKR VDGKWMRELV LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDTTYQ RTRALVRTGM D PRMCSLMQ ...String:
MASQGTKRSY EQMETDGERQ NATEIRASVG KMINGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNRYLE EHPSAGKDP KKTGGPIYKR VDGKWMRELV LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDTTYQ RTRALVRTGM D PRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK RGINDRNFWR GENGRKTRSA YERMCNILKG KFQTAAQRAM MD QVRESRN PGNAEIEDLI FSARSALILR GSVAHKSCLP ACVYGPAVAS GYDFEKEGYS LVGIDPFKLL QNSQVYSLIR PNE NPAHKS QLVWMACHSA AFEDLRLLSF IRGTKVSPRG KLSTRGVQIA SNENMDTMES STLELRSRYW AIRTRSGGNT NQQR ASAGQ ISVQPAFSVQ RNLPFDKSTI MAAFTGNTEG RTSDMRAEII RMMEGAKPEE VSFRGRGVFE LSDEKATNPV VPSFD MSNE GSYFFGDNAE EYDN

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*CP*UP*UP*UP*GP*UP*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 4.948912 KDa
SequenceString:
UCUUUGUCAC CCUGCU

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Macromolecule #3: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*GP*UP*UP...

MacromoleculeName: 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')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 7.7206 KDa
SequenceString:
AGUAGAAACA AGGGUGUUUU UUAU

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265200
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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