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- EMDB-44980: Double helical structure of influenza D RNP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44980
TitleDouble helical structure of influenza D RNP complex
Map datasymmetrized and sharpened map of the double helix
Sample
  • Complex: influenza D virus RNP complex
    • Protein or peptide: Nucleoprotein of influenza D virus
    • RNA: FluD-NS vRNA
KeywordsInfluenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN
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 D virus
Methodhelical reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsPeng R / Chang Y-W
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44980.png

Downloads & links

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Map

FileDownload / File: emd_44980.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetrized and sharpened map of the double helix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 128 pix.
= 276.48 Å		2.16 Å/pix.
x 128 pix.
= 276.48 Å		2.16 Å/pix.
x 128 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.00012649185 - 1.21623
Average (Standard dev.)0.025463268 (±0.10735083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: postprocess sharpened map from half maps

Fileemd_44980_additional_1.map
Annotationpostprocess sharpened map from half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: double helix composite map from local refinement

Fileemd_44980_additional_2.map
Annotationdouble helix composite map from local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: double helix half map 2

Fileemd_44980_half_map_1.map
Annotationdouble helix half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: double helix half map 1

Fileemd_44980_half_map_2.map
Annotationdouble helix half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : influenza D virus RNP complex

EntireName: influenza D virus RNP complex
Components
  • Complex: influenza D virus RNP complex
    • Protein or peptide: Nucleoprotein of influenza D virus
    • RNA: FluD-NS vRNA

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Supramolecule #1: influenza D virus RNP complex

SupramoleculeName: influenza D virus RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza D virus
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: Nucleoprotein of influenza D virus

MacromoleculeName: Nucleoprotein of influenza D virus / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSTKAQTPE EQRAKNAKTI LENIQIYERM CDLFGVSEDD KLIIENSISI ERMIRVVTDK KYQDKKLKNA GSDPEKIANA GKVFCRLVE STAGKCSARL GMALKPNVEA VLTDVLGNEL DRAAVLGKRM GFSAMFKSNL EEVLYQRGKN QLKKRNAAET F TLSQGASL ...String:
MDSTKAQTPE EQRAKNAKTI LENIQIYERM CDLFGVSEDD KLIIENSISI ERMIRVVTDK KYQDKKLKNA GSDPEKIANA GKVFCRLVE STAGKCSARL GMALKPNVEA VLTDVLGNEL DRAAVLGKRM GFSAMFKSNL EEVLYQRGKN QLKKRNAAET F TLSQGASL EARFRPIMEK HLGVGTVVAS IKNILASKKN GNYRNKMVRK PGGNRESWSP LEREISFLNK KLFPGPMRQL CK KFEYLNE QEKQLALNLM LDASLILKPQ VTHKMIMPWS MWLAVKKYAE MNKGSPSLED LAAYSGVRAF MAFNTACYMS KFT IGKGIV GDAEIMENGN DKMQTLAMAC FGLAYEDTGI VAAMISQPMK KRYQLRVGNF NPPEKGTIKG TSAGYFHKWA EFGN RLPFN SFGTGESKQI SNSGVFAVQR PSTTNIQRLA ELMARNTGET SDNFTQLVQK IREQVGAFAD QKANLREFTG GYIYD ITDV TKSNPKIPQL GGDSFFFEFT GSDVPRTGAK RRVGGADDVT PGTSQPKKRG RQGAGAESSM DIETVGED

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Macromolecule #2: FluD-NS vRNA

MacromoleculeName: FluD-NS vRNA / type: rna / ID: 2
Source (natural)Organism: Influenza D virus
SequenceString: AGCAGUAGCA AGGGGUUUUU UCAUACUAAA GAACGAAUAC AUUCUUUUAA CAUUGAAAUU GUUCUCGAAA CUGACUUGAU UUCAUCCAAA GCGGCCCUCA UAUCCUGGUU AGUCAAAGAG UUCACCAUCG CUACUCCCAG CUUGGAUUUC AACCUUAUCA AUGACACCAA ...String:
AGCAGUAGCA AGGGGUUUUU UCAUACUAAA GAACGAAUAC AUUCUUUUAA CAUUGAAAUU GUUCUCGAAA CUGACUUGAU UUCAUCCAAA GCGGCCCUCA UAUCCUGGUU AGUCAAAGAG UUCACCAUCG CUACUCCCAG CUUGGAUUUC AACCUUAUCA AUGACACCAA GCAACUCCUG AACCUCUCCA GUAGUUGCGC CUUCUCUUCU CCAGAAGGGA UCUGUUUCAC AUCCAGAUUU GUAUCGUCUG AUUUCAUCUC UAGAUUCCGC AUCAACGGCA ACAACAAGUC CACUUCUCCA AAUUCUGAGU AUCUUUCGUA CUGACUUCUC UGGGUCAUCU CCUCUACGGA AAUUCUUAAG GCAGUAAGCU GGUUUCUCAG UGUUUCUGCA AAAGAGCACA AUGAUUUCUC CCAUGUCGGU CACUAAUAGU UCAGCAGUUU UUACAAAGCA AUUGCAGUUC CGAUAUUUUA CUCCAAAGAC UUCUCCUUGU CUUAUGAGCU UUGGCUCAUA CAGAGUGUCA AUGGUACAUG GGCUUAGAUA GAAAGGGUUU CCUCCUAAGG GAUAGAUAAU GUUCUUCCCC AAUUCAACAG CAUGAGUCUC CUCUGGUUUU CUUAAGGCAG CAAUAGUAGU GAAUCCUAGA AUUUCUCUAC CUUCAGCCAC UGCAUCUUCC CAAGUUCUCG GUUCAUAAAC CUGUUCGACU CUCAGUGAAU UCUCAGCAGA CUUUCUCAUU UUCUCGAAAG UCAUUAACCC AGAGGAAUCC AUCCAGCUGG CUGCGCCCAA UGCCAAUUCG GAGAUUGCUG CUCUGAUAUU UGUUGUGUUC ACUGACUUAU UUUCAGACAU AUUGAAAUUG UACACCCCUG CUUAUGCU

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 1x PBS
VitrificationCryogen name: ETHANE-PROPANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 3.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 26.87 Å
Applied symmetry - Helical parameters - Δ&Phi: 61.64 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 44679
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 3500000 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: NONE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5n2u


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross correlation coefficient
Output model

PDB-9c4h:
Double helical structure of influenza D RNP complex

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