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- EMDB-18872: Influenza A/H7N9 polymerase in pre-initiation state, intermediate... -

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Basic information

Entry
Database: EMDB / ID: EMD-18872
TitleInfluenza A/H7N9 polymerase in pre-initiation state, intermediate conformation (I) with PB2-C(I), ENDO(T), and Pol II pS5 CTD peptide mimic bound in site 1A/2A
Map data
Sample
  • Complex: Heterotrimeric influenza polymerase
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: 3' vRNA end (51-mer vRNA loop)
    • Protein or peptide: RNA Pol II CTD 6 repeats (site 1A/2A)
KeywordsViral polymerase / VIRAL PROTEIN
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsArragain B / Cusack S
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0028 France
CitationJournal: Nat Commun / Year: 2024
Title: The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome.
Authors: Tim Krischuns / Benoît Arragain / Catherine Isel / Sylvain Paisant / Matthias Budt / Thorsten Wolff / Stephen Cusack / Nadia Naffakh /
Abstract: The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation ...The current model is that the influenza virus polymerase (FluPol) binds either to host RNA polymerase II (RNAP II) or to the acidic nuclear phosphoprotein 32 (ANP32), which drives its conformation and activity towards transcription or replication of the viral genome, respectively. Here, we provide evidence that the FluPol-RNAP II binding interface, beyond its well-acknowledged function in cap-snatching during transcription initiation, has also a pivotal role in replication of the viral genome. Using a combination of cell-based and in vitro approaches, we show that the RNAP II C-terminal-domain, jointly with ANP32, enhances FluPol replication activity. We observe successive conformational changes to switch from a transcriptase to a replicase conformation in the presence of the bound RNPAII C-terminal domain and propose a model in which the host RNAP II is the anchor for transcription and replication of the viral genome. Our data open new perspectives on the spatial coupling of viral transcription and replication and the coordinated balance between these two activities.
History
DepositionNov 9, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18872.png

Downloads & links

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Map

FileDownload / File: emd_18872.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.01785773 - 0.03788967
Average (Standard dev.)0.0000560569 (±0.0008950936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18872_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_18872_additional_1.map
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Half map: #1

Fileemd_18872_half_map_1.map
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Half map: #2

Fileemd_18872_half_map_2.map
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Sample components

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Entire : Heterotrimeric influenza polymerase

EntireName: Heterotrimeric influenza polymerase
Components
  • Complex: Heterotrimeric influenza polymerase
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: 3' vRNA end (51-mer vRNA loop)
    • Protein or peptide: RNA Pol II CTD 6 repeats (site 1A/2A)

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Supramolecule #1: Heterotrimeric influenza polymerase

SupramoleculeName: Heterotrimeric influenza polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

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Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Molecular weightTheoretical: 84.354188 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHG SGSMEDFVRQ CFNPMIVELA EKAMKEYGED PKIETNKFAS ICTHLEVCFM YSDFHFIDER GESTIIESGD PNVLLKHRF EIIEGRDRTM AWTVVNSICN TTGVEKPKFL PDLYDYKENR FIEIGVTRRE VHIYYLEKAN KIKSEKTHIH I FSFTGEEM ...String:
MHHHHHHHHG SGSMEDFVRQ CFNPMIVELA EKAMKEYGED PKIETNKFAS ICTHLEVCFM YSDFHFIDER GESTIIESGD PNVLLKHRF EIIEGRDRTM AWTVVNSICN TTGVEKPKFL PDLYDYKENR FIEIGVTRRE VHIYYLEKAN KIKSEKTHIH I FSFTGEEM ATKADYTLDE ESRARIKTRL FTIRQEMASR GLWDSFRQSE RGEETIEERF EITGTMRRLA DQSLPPNFSS LE NFRAYVD GFEPNGCIEG KLSQMSKEVN ARIEPFLRTT PRPLRLPDGP PCSQRSKFLL MDALKLSIED PSHEGEGIPL YDA IKCMKT FFGWKEPNII KPHEKGINPN YLLTWKQVLA ELQDIKNEEK IPRTKNMKKT SQLKWALGEN MAPEKVDFED CKDV NDLKQ YDSDEPEPRS LACWIQSEFN KACELTDSSW VELDEIGEDV APIEHIASMR RNYFTAEVSH CRATEYIMKG VYINT ALLN ASCAAMDDFQ LIPMISKCIT KEGRRKTNLY GFIIKGRSHL RNDTDVVNFV SMEFSLTDPR LEPHKWEKYC VLEIGD MLL RTAVGQVSRP MFLYVRTNGT SKIKMKWGME MRRCLLQSLQ QIESMIEAES SVKEKDLTKE FFENKSETWP IGESPKG VE EGSIGKVCRT LLAKSVFNSL YASPQLEGFS AESRKLLLIV QALRDNLEPG TFDLEGLYEA IEECLINDPW VLLNASWF N SFLTHALR

UniProtKB: Polymerase acidic protein

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Macromolecule #2: RNA-directed RNA polymerase catalytic subunit

MacromoleculeName: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Molecular weightTheoretical: 86.424031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDVNPTLLFL KVPVQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHKYS EKGKWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEIVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK ...String:
MDVNPTLLFL KVPVQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHKYS EKGKWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEIVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK DVMDSMDKEE MEITTHFQRK RRVRDNMTKK MVTQRTIGKK KQRLNKRSYL IRALTLNTMT KDAERGKLKR RA IATPGMQ IRGFVYFVEA LARSICEKLE QSGLPVGGNE KKAKLANVVR KMMTNSQDTE LSFTITGDNT KWNENQNPRM FLA MITYIT RNQPEWFRNV LSIAPIMFSN KMARLGKGYM FESKSMKLRT QVPAEMLANI DLKYFNKSTR EKIEKIRPLL IDGT ASLSP GMMMGMFNML STVLGVSILN LGQKKYTKTT YWWDGLQSSD DFALIVNAPN HEGIQAGVDR FYRTCKLVGI NMSKK KSYI NRTGTFEFTS FFYRYGFVAN FSMELPSFGV SGINESADMS VGVTVIKNNM INNDLGPATA QMALQLFIKD YRYTYR CHR GDTQIQTRRA FELGKLWEQT RSKAGLLVSD GGPNLYNIRN LHIPEVCLKW ELMDEDYQGR LCNPMNPFVS HKEIDSV NN AVVMPAHGPA KSMEYDAVAT THSWIPKRNR SILNTSQRGI LEDEQMYQKC CNLFEKFFPS SSYRRPVGIS SMVEAMVS R ARIDARIDFE SGRIKKEEFA EIMKICSTIE ELRRQK

UniProtKB: RNA-directed RNA polymerase catalytic subunit

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Macromolecule #3: Polymerase basic protein 2

MacromoleculeName: Polymerase basic protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Molecular weightTheoretical: 89.037578 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQRQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSTV HYPKVYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF ...String:
MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQRQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSTV HYPKVYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF PNEVGARILT SESQLTITKE KKKELQDCKI APLMVAYMLE RELVRKTRFL PVAGGTSSVY IEVLHLTQGT CW EQMYTPG GEVRNDDVDQ SLIIAARNIV RRATVSADPL ASLLEMCHST QIGGVRMVDI LRQNPTEEQA VDICKAAMGL RIS SSFSFG GFTFKRTSGS SVKREEEVLT GNLQTLKIRV HEGYEEFTMV GRRATAILRK ATRRLIQLIV SGKDEQSIAE AIIV AMVFS QEDCMIKAVR GDLNFVNRAN QRLNPMHQLL RHFQKDAKVL FQNWGIEPID NVMGMIGILP DMTPSTEMSL RGVRV SKMG VDEYSSTERV VVSIDRFLRV RDQRGNVLLS PEEVSETQGT EKLTITYSSS MMWEINGPES VLVNTYQWII RNWENV KIQ WSQDPTMLYN KMEFEPFQSL VPKAARGQYS GFVRVLFQQM RDVLGTFDTV QIIKLLPFAA APPEQSRMQF SSLTVNV RG SGMRIVVRGN SPVFNYNKAT KRLTVLGKDA GALMEDPDEG TAGVESAVLR GFLILGKENK RYGPALSINE LSNLAKGE K ANVLIGQGDV VLVMKRKRDS SILTDSQTAT KRIRMAINGW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: Polymerase basic protein 2

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Macromolecule #5: RNA Pol II CTD 6 repeats (site 1A/2A)

MacromoleculeName: RNA Pol II CTD 6 repeats (site 1A/2A) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.736352 KDa
SequenceString:
YSPT(SEP)PSYSP TSPSYSPT(SEP)P SYSPT(SEP)PSYS PT(SEP)PSYSPT(SEP) PS

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Macromolecule #4: 3' vRNA end (51-mer vRNA loop)

MacromoleculeName: 3' vRNA end (51-mer vRNA loop) / type: rna / ID: 4 / Number of copies: 2
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Molecular weightTheoretical: 16.093369 KDa
SequenceString:
AGUAGAAACA AGGGUGUAUU UUCCCCUCUU UUUGUUUCCC CUGCUUUUGC U

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17121
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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