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- EMDB-44983: Structure of the loop end of influenza D virus RNP complex, class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-44983
TitleStructure of the loop end of influenza D virus RNP complex, class 2
Map dataloop-end class 2 sharpened map
Sample
  • Complex: influenza D virus RNP complex
    • Protein or peptide: Influenza D virus nucleoprotein
    • RNA: FluD-NS vRNA
KeywordsInfluenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN
Biological speciesInfluenza D virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 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_44983.png

Downloads & links

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Map

FileDownload / File: emd_44983.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationloop-end class 2 sharpened map
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: 0.22
Minimum - Maximum-0.30762434 - 2.2601001
Average (Standard dev.)0.0125268055 (±0.07688189)
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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Half map: loop-end class 2 half map 2

Fileemd_44983_half_map_1.map
Annotationloop-end class 2 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: loop-end class 2 half map 1

Fileemd_44983_half_map_2.map
Annotationloop-end class 2 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: Influenza D virus nucleoprotein
    • 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: 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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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
Processingsingle particle 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

Particle selectionNumber selected: 2000000
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 49437
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - 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
RefinementProtocol: RIGID BODY FIT / Target criteria: cross correlation coefficient

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