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- EMDB-44997: The nucleoprotein subunits next the polymerase in the middle of i... -

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Basic information

Entry
Database: EMDB / ID: EMD-44997
TitleThe nucleoprotein subunits next the polymerase in the middle of influenza D RNP, piece 1
Map datacomposite map with local averaging of individual NP subunit
Sample
  • Complex: Influenza D virus RNP complex
    • Protein or peptide: Influenza D virus nucleoprotein
KeywordsInfluenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN
Biological speciesInfluenza D virus
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 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_44997.png

Downloads & links

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Map

FileDownload / File: emd_44997.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map with local averaging of individual NP subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.26884145 - 1.04938
Average (Standard dev.)0.010537228 (±0.127039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 174.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: postprocessed map without local averaging of NP subunit

Fileemd_44997_additional_1.map
Annotationpostprocessed map without local averaging of NP subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1

Fileemd_44997_half_map_1.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_44997_half_map_2.map
Annotationhalf 2
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: Influenza D virus nucleoprotein

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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: Influenza D virus nucleoprotein

MacromoleculeName: Influenza D virus nucleoprotein / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 1x PBS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
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 - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 4220
ExtractionNumber tomograms: 503 / Number images used: 4220 / Software - Name: Warp (ver. 1.09)
CTF correctionSoftware - Name: Warp (ver. 1.09) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / 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: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

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