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Yorodumi- EMDB-9582: Structure of influenza D virus polymerase bound to vRNA promoter ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9582 | |||||||||
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Title | Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3) | |||||||||
Map data | structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3) | |||||||||
Sample |
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Function / homology | Function and homology information RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / RNA binding Similarity search - Function | |||||||||
Biological species | Influenza D virus / Influenza D virus (D/swine/Oklahoma/1334/2011) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Peng Q / Peng R / Qi J / Gao GF / Shi Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Microbiol / Year: 2019 Title: Structural insight into RNA synthesis by influenza D polymerase. Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi / Abstract: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9582.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-9582-v30.xml emd-9582.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9582_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_9582.png | 105.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9582 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9582 | HTTPS FTP |
-Related structure data
Related structure data | 6kuuMC 9577C 9578C 9579C 9580C 9581C 9887C 9888C 6kujC 6kukC 6kupC 6kurC 6kutC 6kuvC 6kv5C 6abg M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9582.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Influenza D virus polymerase boud to vRNA promoter
Entire | Name: Influenza D virus polymerase boud to vRNA promoter |
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Components |
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-Supramolecule #1: Influenza D virus polymerase boud to vRNA promoter
Supramolecule | Name: Influenza D virus polymerase boud to vRNA promoter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Influenza D virus |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
Molecular weight | Experimental: 270 KDa |
-Macromolecule #1: Polymerase 3
Macromolecule | Name: Polymerase 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza D virus (D/swine/Oklahoma/1334/2011) / Strain: D/swine/Oklahoma/1334/2011 |
Molecular weight | Theoretical: 83.036086 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPL RNLADIFDRK TRRFLEVGIT KRESDEYYQE KFNKIGNDMD IHVFTYEGKY FSNNPNGLED IQKTRIFTFL S FVSDELRK ...String: MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPL RNLADIFDRK TRRFLEVGIT KRESDEYYQE KFNKIGNDMD IHVFTYEGKY FSNNPNGLED IQKTRIFTFL S FVSDELRK ENMFTEMYVT EEGAPELEMY KSKLFIAMRD ESVPLPYINY EHLRTRCETF KRNQAECEAK VADVASRLKI KL EHLEENK LRPLEIPKEK EAPYTHKFLM KDAWFFAKPH DSERAQPQQI LYDFFEAANM GFMTTSPKPI FGKQGLMYHS LWG QTKRAI KDKRNELEPS EQRDFLCGIG RASKKIQEDK WQESREEEFK QEETKGAAKR GFPTWFNEEW LWAMRDSGDG DNKI GDWIP MAEMPPCKNE MEDYAKKMCE ELESKIQGTN CAREMSKLIH TIGSLHTECR NFPGKVKIVP IYCRGTLRGE STDCL FGIA IKGKSHLNKD DGMYTVVTFE FSTEEPNPSK HEKYTVFEAG TVPVEAVVLT PKRERVLKEK KLFLYCRTTG MSKLKN DWF SKCRRCLIPT METVEQIVLK ECALKEENRV SEMLENKRAW IAHENGENLT RLVSTKLKDL CRMLIVTQFY YCIYNDN QL EGFCNEQKKF LMFLQADKDS KSAFTFNQKG LYEKIEECIV SNPLCIFLAD RLNKLFLVAK SNGAKYFE |
-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 D virus (D/swine/Oklahoma/1334/2011) / Strain: D/swine/Oklahoma/1334/2011 |
Molecular weight | Theoretical: 86.138844 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINF MLSLAEMLEE KMGKGFFKFC ANEAEAEILK MHFSKLTEGR QTYDWTSERN MPAATALQLT VDAIQETQGT F KGTTMVEY ...String: MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINF MLSLAEMLEE KMGKGFFKFC ANEAEAEILK MHFSKLTEGR QTYDWTSERN MPAATALQLT VDAIQETQGT F KGTTMVEY CNKILEMMDW PEVKFKKVRM IVQRHWDPKT KKEIKMKSPT LMITKIGREE FIKRICTINT MAKDGERGKY KR RAIATPG MGIRPFSKIV ETLAQKICER LAESGLPVGG NEKKAKLKTT VSSTNSKLQE GQFMVNITGD NSKWNECQQP EAY LAMLAY ITKDSSNLMK DLCSVAPTLF CNKYVKMGQG FRAKNKRKTK EIVIPAKKMK ERKELMNAEW RDLFETIEPY MDGE CCFLG GGMLMGMFNM LSTVFGVMTL NYREEALARR NCYWTGLQSS DDFVLFCISR TWPEMEMTIL KFIAVCKLMG INMSL EKSY GCLPELFEFT SMFFSGDFVS NIALELPAFT TAGMNEGTDF TAAMSVIRTN MINNGLSPGT ALMALRICLQ EFRATY RVH PYDSGVKNHR MKIIRKFIET IENKDGLLIS DGGKLMNNIS SLHIPEEILK EDLMDPSYRN RVFNPRNPFT QFEKTVD IF KASGPIRVEE NEAVVSTHSF RTRSNRTLLN TDMRAMALEE KRYQVVCNMY RSVFESADVN TPIGSMSMGE AIEAKILD R ARTQFENGII GGEEYSEIKR LIEDAKRQRL SV |
-Macromolecule #3: Polymerase PB2
Macromolecule | Name: Polymerase PB2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza D virus (D/swine/Oklahoma/1334/2011) / Strain: D/swine/Oklahoma/1334/2011 |
Molecular weight | Theoretical: 29.338217 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDV SKLGMVLASP AAITYWNFCG PGVDNSSVIK DVYKAKFMKK ERWRETLWGP MNFELVGKQR RVVETQPVEI K LNQKEIKE ...String: MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDV SKLGMVLASP AAITYWNFCG PGVDNSSVIK DVYKAKFMKK ERWRETLWGP MNFELVGKQR RVVETQPVEI K LNQKEIKE LTMWVLFEDE ANLASKFIQE NFSLVLSLRE LYKGKAVNKD VAAFMIAHQF SPEKRFLPTF GPIRPERMEL LH CLGGDFW KIEAVTA |
-Macromolecule #4: RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3')
Macromolecule | Name: RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3') type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.337563 KDa |
Sequence | String: CUCCUGCUUA UGCU |
-Macromolecule #5: RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3')
Macromolecule | Name: RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3') type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.918042 KDa |
Sequence | String: AGCAGUAGCA AGGAG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4.1) |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: 6ab7 Details: Influenza D virus plolymerase |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0) |
Final 3D classification | Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 120864 |
FSC plot (resolution estimation) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6kuu: |