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Yorodumi- EMDB-17755: Influenza A/H7N9 polymerase in replicase-like conformation in pre... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17755 | |||||||||
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Title | Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with Pol II pS5 CTD peptide mimic bound in site 1A/2A | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Viral polymerase / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / host cell nucleus / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Arragain B / Cusack S | |||||||||
Funding support | France, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17755.map.gz | 14 MB | EMDB map data format | |
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Header (meta data) | emd-17755-v30.xml emd-17755.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17755_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_17755.png | 48.8 KB | ||
Masks | emd_17755_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-17755.cif.gz | 7.9 KB | ||
Others | emd_17755_half_map_1.map.gz emd_17755_half_map_2.map.gz | 141.5 MB 141 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17755 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17755 | HTTPS FTP |
-Validation report
Summary document | emd_17755_validation.pdf.gz | 946.4 KB | Display | EMDB validaton report |
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Full document | emd_17755_full_validation.pdf.gz | 946 KB | Display | |
Data in XML | emd_17755_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | emd_17755_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17755 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17755 | HTTPS FTP |
-Related structure data
Related structure data | 8pm0MC 8pnpC 8pnqC 8pohC 8r3kC 8r3lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17755.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17755_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17755_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17755_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A/H7N9 polymerase in replicase-like conformation in pre...
Entire | Name: Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with Pol II pS5 CTD peptide mimic bound in site 1A/2A |
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Components |
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-Supramolecule #1: Influenza A/H7N9 polymerase in replicase-like conformation in pre...
Supramolecule | Name: Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with Pol II pS5 CTD peptide mimic bound in site 1A/2A type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
-Macromolecule #1: Polymerase acidic protein
Macromolecule | Name: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
Molecular weight | Theoretical: 84.354188 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #2: RNA-directed RNA polymerase catalytic subunit
Macromolecule | Name: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
Molecular weight | Theoretical: 86.496156 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 FELKKLWEQT 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 |
-Macromolecule #3: Polymerase basic protein 2
Macromolecule | Name: Polymerase basic protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
Molecular weight | Theoretical: 89.037578 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #5: RNA Pol II CTD 6 repeats (site 1A/2A)
Macromolecule | Name: RNA Pol II CTD 6 repeats (site 1A/2A) / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 4.816331 KDa |
Sequence | String: YSPT(SEP)PSYSP T(SEP)PSYSPT(SEP)P SYSPT(SEP)PSYS PT(SEP)PSYSPT(SEP) PS |
-Macromolecule #4: 51-mer vRNA loop (v51_mut_S)
Macromolecule | Name: 51-mer vRNA loop (v51_mut_S) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
Molecular weight | Theoretical: 16.093369 KDa |
Sequence | String: AGUAGAAACA AGGGUGUAUU UUCCCCUCUU UUUGUUUCCC CUGCUUUUGC U |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Grid | Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |