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- EMDB-45187: Subtomogram averaging of the polymerase end of influenza RNP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45187
TitleSubtomogram averaging of the polymerase end of influenza RNP complex
Map datacomposite map produced by stitching focus average maps, with local average of individual NP subunit
Sample
  • Complex: Influenza D virus RNP complex
    • Protein or peptide: Influenza D virus nucleoprotein
    • Protein or peptide: Influenza D virus polymerase P3 subunit
    • Protein or peptide: Influenza D virus polymerase PB1 subunit
    • Protein or peptide: Influenza D virus polymerase PB2 subunit
    • RNA: Influenza D virus NS vRNA segment
Keywordsinfluenza virus / RNP complex / polymerase / nucleoprotein / VIRAL PROTEIN
Biological speciesInfluenza D virus
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 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
DepositionJun 4, 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_45187.png

Downloads & links

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Map

FileDownload / File: emd_45187.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map produced by stitching focus average maps, with local average of individual NP subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 128 pix.
= 348.16 Å		2.72 Å/pix.
x 128 pix.
= 348.16 Å		2.72 Å/pix.
x 128 pix.
= 348.16 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: 0.238
Minimum - Maximum0.0 - 0.87075186
Average (Standard dev.)0.010821163 (±0.05658944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 348.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: postprocessed map from half maps

Fileemd_45187_additional_1.map
Annotationpostprocessed map from half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_45187_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_45187_half_map_2.map
Annotationhalf map 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
    • Protein or peptide: Influenza D virus polymerase P3 subunit
    • Protein or peptide: Influenza D virus polymerase PB1 subunit
    • Protein or peptide: Influenza D virus polymerase PB2 subunit
    • RNA: Influenza D virus NS vRNA segment

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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

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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: Influenza D virus polymerase P3 subunit

MacromoleculeName: Influenza D virus polymerase P3 subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPLR NLADIFDRKT RRFLEVGITK RESDEYYQEK FNKIGNDMDI HVFTYEGKYF SNNPNGLEDI QKTRIFTFLS FVSDELRKEN ...String:
MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPLR NLADIFDRKT RRFLEVGITK RESDEYYQEK FNKIGNDMDI HVFTYEGKYF SNNPNGLEDI QKTRIFTFLS FVSDELRKEN MFTEMYVTEE GAPELEMYKS KLFIAMRDES VPLPYINYEH LRTRCETFKR NQAECEAKVA DVASRLKIKL EHLEENKLRP LEIPKEKEAP YTHKFLMKDA WFFAKPHDSE RAQPQQILYD FFEAANMGFM TTSPKPIFGK QGLMYHSLWG QTKRAIKDKR NELEPSEQRD FLCGIGRASK KIQEDKWQES REEEFKQEET KGAAKRGFPT WFNEEWLWAM RDSGDGDNKI GDWIPMAEMP PCKNEMEDYA KKMCEELESK IQGTNCAREM SKLIHTIGSL HTECRNFPGK VKIVPIYCRG TLRGESTDCL FGIAIKGKSH LNKDDGMYTV VTFEFSTEEP NPSKHEKYTV FEAGTVPVEA VVLTPKRERV LKEKKLFLYC RTTGMSKLKN DWFSKCRRCL IPTMETVEQI VLKECALKEE NRVSEMLENK RAWIAHENGE NLTRLVSTKL KDLCRMLIVT QFYYCIYNDN QLEGFCNEQK KFLMFLQADK DSKSAFTFNQ KGLYEKIEEC IVSNPLCIFL ADRLNKLFLV AKSNGAKYFE

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Macromolecule #3: Influenza D virus polymerase PB1 subunit

MacromoleculeName: Influenza D virus polymerase PB1 subunit / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINFM LSLAEMLEEK MGKGFFKFCA NEAEAEILKM HFSKLTEGRQ TYDWTSERNM PAATALQLTV DAIQETQGTF KGTTMVEYCN ...String:
MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINFM LSLAEMLEEK MGKGFFKFCA NEAEAEILKM HFSKLTEGRQ TYDWTSERNM PAATALQLTV DAIQETQGTF KGTTMVEYCN KILEMMDWPE VKFKKVRMIV QRHWDPKTKK EIKMKSPTLM ITKIGREEFI KRICTINTMA KDGERGKYKR RAIATPGMGI RPFSKIVETL AQKICERLAE SGLPVGGNEK KAKLKTTVSS TNSKLQEGQF MVNITGDNSK WNECQQPEAY LAMLAYITKD SSNLMKDLCS VAPTLFCNKY VKMGQGFRAK NKRKTKEIVI PAKKMKERKE LMNAEWRDLF ETIEPYMDGE CCFLGGGMLM GMFNMLSTVF GVMTLNYREE ALARRNCYWT GLQSSDDFVL FCISRTWPEM EMTILKFIAV CKLMGINMSL EKSYGCLPEL FEFTSMFFSG DFVSNIALEL PAFTTAGMNE GTDFTAAMSV IRTNMINNGL SPGTALMALR ICLQEFRATY RVHPYDSGVK NHRMKIIRKF IETIENKDGL LISDGGKLMN NISSLHIPEE ILKEDLMDPS YRNRVFNPRN PFTQFEKTVD IFKASGPIRV EENEAVVSTH SFRTRSNRTL LNTDMRAMAL EEKRYQVVCN MYRSVFESAD VNTPIGSMSM GEAIEAKILD RARTQFENGI IGGEEYSEIK RLIEDAKRQR LSV

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Macromolecule #4: Influenza D virus polymerase PB2 subunit

MacromoleculeName: Influenza D virus polymerase PB2 subunit / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDVS KLGMVLASPA AITYWNFCGP GVDNSSVIKD VYKAKFMKKE RWRETLWGPM NFELVGKQRR VVETQPVEIK LNQKEIKELT ...String:
MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDVS KLGMVLASPA AITYWNFCGP GVDNSSVIKD VYKAKFMKKE RWRETLWGPM NFELVGKQRR VVETQPVEIK LNQKEIKELT MWVLFEDEAN LASKFIQENF SLVLSLRELY KGKAVNKDVA AFMIAHQFSP EKRFLPTFGP IRPERMELLH CLGGDFWKIE AVTAGSLNEE QKKRDVRAVA RKICLRASVD LFTPAEKIRD YIASVTMRFG TVERTFEDVI RNSDDISAEV TLCKAALGCE LGKSMSFGNL NLRKVSGEAE TMEKTVYWGL KPIKYKCWRG EETFYCELRK VTCMFRRSEG LDWANIGPGS PEERRELLAM VMIFCRDGRF FESAPVNIDE SFFRTRLNKE IPYQYVLLKW VRQSRDNLDA LLSTRGLIPA HIGQFGKGMG IDGSSSSSMV YKGVMLSKTP IDIVESKEKH RLFLNDNIEA VTERGAMVAS IMDLSEDNRE TFNDVTFNHV DLAVLKDEKT AIIKIYRSLV ERINTDDDGL PALIMGKRYL ELYQLDEVKD AVGLIPKRML GAYSYQARQL IQSQIKNDSY SLPEIIKLLP FCYSPPKKML FDGTFHFKNQ MYVRPGINTN LFSFSKTDKS KIYVNGSAVK IKLVLGDDEM DTSLAFVEGF QVCEYDPRAP LIPRRDLRLI GFGKKVRVFV GQGQEKTLVR TSSKRAASHD VSKNIRRMRL EV

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Macromolecule #5: Influenza D virus NS vRNA segment

MacromoleculeName: Influenza D virus NS vRNA segment / type: rna / ID: 5
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
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 / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.8 µm
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: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 3440
ExtractionNumber tomograms: 503 / Number images used: 3440
Software:
Namedetails
UCSF ChimeraX (ver. 1.3)particle picking
Warp (ver. 1.09)subtomogram reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5n2u

source_name: PDB, initial_model_type: experimental model

7nhx

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

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