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Yorodumi- EMDB-10357: Bat Influenza A polymerase product dissociation complex using 44-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10357 | |||||||||
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Title | Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with mutated oligo(U) sequence | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Influenza / polymerase / viral transcription / RNA / 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 / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / host cell cytoplasm / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / host cell cytoplasm / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
Authors | Wandzik JM / Kouba T | |||||||||
Funding support | France, 1 items
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Citation | Journal: Cell / Year: 2020 Title: A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Authors: Joanna M Wandzik / Tomas Kouba / Manikandan Karuppasamy / Alexander Pflug / Petra Drncova / Jan Provaznik / Nayara Azevedo / Stephen Cusack / Abstract: Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). ...Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP. | |||||||||
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_10357.map.gz | 108.4 MB | EMDB map data format | |
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Header (meta data) | emd-10357-v30.xml emd-10357.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10357_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_10357.png | 139.9 KB | ||
Filedesc metadata | emd-10357.cif.gz | 7.1 KB | ||
Others | emd_10357_additional.map.gz emd_10357_half_map_1.map.gz emd_10357_half_map_2.map.gz | 55.7 MB 91.3 MB 91.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10357 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10357 | HTTPS FTP |
-Validation report
Summary document | emd_10357_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_10357_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_10357_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_10357_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10357 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10357 | HTTPS FTP |
-Related structure data
Related structure data | 6t0rMC 6szuC 6szvC 6t0nC 6t0sC 6t0uC 6t0vC 6t0wC 6t2cC 6tu5C 6tw1C 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_10357.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8127 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: LocScale map
File | emd_10357_additional.map | ||||||||||||
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Annotation | LocScale map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10357_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10357_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bat Influenza A polymerase product dissociation complex using 44-...
Entire | Name: Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with mutated oligo(U) sequence |
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Components |
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-Supramolecule #1: Bat Influenza A polymerase product dissociation complex using 44-...
Supramolecule | Name: Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with mutated oligo(U) sequence type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Polymerase
Supramolecule | Name: Polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) |
-Supramolecule #3: Nucleic acid
Supramolecule | Name: Nucleic acid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: synthetic construct (others) |
-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/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) |
Molecular weight | Theoretical: 85.49093 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSHHHHHHHH GSGSMENFVR TNFNPMILER AEKTMKEYGE NPQNEGNKFA AISTHMEVCF MYSDFHFIDL EGNTIVKEND DDNAMLKHR FEIIEGQERN IAWTIVNSIC NMTENSKPRF LPDLYDYKTN KFIEIGVTRR KVEDYYYEKA SKLKGENVYI H IFSFDGEE ...String: GSHHHHHHHH GSGSMENFVR TNFNPMILER AEKTMKEYGE NPQNEGNKFA AISTHMEVCF MYSDFHFIDL EGNTIVKEND DDNAMLKHR FEIIEGQERN IAWTIVNSIC NMTENSKPRF LPDLYDYKTN KFIEIGVTRR KVEDYYYEKA SKLKGENVYI H IFSFDGEE MATDDEYILD EESRARIKTR LFVLRQELAT AGLWDSFRQS EKGEETLEEE FSYPPTFQRL ANQSLPPSFK DY HQFKAYV SSFKANGNIE AKLGAMSEKV NAQIESFDPR TIRELELPEG KFCTQRSKFL LMDAMKLSVL NPAHEGEGIP MKD AKACLD TFWGWKKATI IKKHEKGVNT NYLMIWEQLL ESIKEMEGKF LNLKKTNHLK WGLGEGQAPE KMDFEDCKEV PDLF QYKSE PPEKRKLASW IQSEFNKASE LTNSNWIEFD ELGNDVAPIE HIASRRRNFF TAEVSQCRAS EYIMKAVYIN TALLN SSCT AMEEYQVIPI ITKCRDTSGQ RRTNLYGFII KGRSHLRNDT DVVNFISLEF SLTDPRNEIH KWEKYCVLEI GDMEIR TSI STIMKPVYLY VRTNGTSKIK MKWGMEMRRC LLQSLQQVES MIEAESAVKE KDMTEPFFRN RENDWPIGES PQGIEKG TI GKVCRVLLAK SVFNSIYASA QLEGFSAESR KLLLLIQAFR DNLDPGTFDL KGLYEAIEEC IINDPWVLLN ASWFNSFL K AVQLSMGSGS GENLYFQ 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/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) |
Molecular weight | Theoretical: 87.936312 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSGSGSGSGM DVNPMLIFLK VPVQNAISTT FPYTGDPPYS HGTGTGYTMD TVIRTHDYSS RGIWKTNSET GAQQLNPIDG PLPEDNEPS GYAQTDCVLE LIEGLDRSHP GLFETACQET IDAIQQTRVD KLTQGRQTYD WTLNRNQPAA TALANTIEVF R KNGYKLNE ...String: GSGSGSGSGM DVNPMLIFLK VPVQNAISTT FPYTGDPPYS HGTGTGYTMD TVIRTHDYSS RGIWKTNSET GAQQLNPIDG PLPEDNEPS GYAQTDCVLE LIEGLDRSHP GLFETACQET IDAIQQTRVD KLTQGRQTYD WTLNRNQPAA TALANTIEVF R KNGYKLNE SGRLIDFLKD VLLSFENDSM EVTTHFQKKK RIRDNHSKKM ITQRTIGKKR VKLTKKNYLI RALTLNTMTK DA ERGKLKR RAIATPGMQI RGFVYFVELL ARNICERLEQ SGLPVGGNEK KAKLANVIKK MMAKSTDEEL SYTITGDNTK WNE NQNPRI FLAMVLRITA GQPEWFRDLL AVAPIMFSNK VARLGRGYMF ESKSMHLRTQ ISAENLSDIN LRYFNEDTKK KIEK IRHLM VEGTASLSPG MMMGMFNMLS TVLGVSVLNL GQREILKRTY WWDGLQSSDD FALIINGHFK EDIQQGVNHF YRTCK LVGI NMSQKKSYIN KTGTFEFTSF FYRYGFVANF SMELPSFGVA GNNESADMSI GTTVIKTNMI NNDLGPATAQ MAIQLF IKD YRYTYRCHRG DTNLETRRTK SIKRLWTETI SKAGLLVADG GPNPYNLRNL HIPEVCLKWS LMDPDYRGRL CNPNNPF VH HMEVESTNLA VVMPAHGPAK SLEYDAVATT HSWTPKRNRS ILNTNQRGIL EDERIYQKCC QVFEKFFPSS TYRRPIGM A SMLDAMLSRA RIDARIDLES GRISSQDFSE ITNTCKAIEA LKRQGSGSGE NLYFQ 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/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) |
Molecular weight | Theoretical: 91.027141 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSGSGSGSGM ERIKELMEMV KNSRMREILT TTSVDHMAVI KKYTSGRQEK NPALRMKWMM AMKYPISASS RIREMIPEKD EDGNTLWTN TKDAGSNRVL VSPNAVTWWN RAGPVSDVVH YPRVYKMYFD RLERLTHGTF GPVKFYNQVK VRKRVDINPG H KDLTSREA ...String: GSGSGSGSGM ERIKELMEMV KNSRMREILT TTSVDHMAVI KKYTSGRQEK NPALRMKWMM AMKYPISASS RIREMIPEKD EDGNTLWTN TKDAGSNRVL VSPNAVTWWN RAGPVSDVVH YPRVYKMYFD RLERLTHGTF GPVKFYNQVK VRKRVDINPG H KDLTSREA QEVIMEVVFP NEVGARTLSS DAQLTITKEK KEELKNCKIS PIMVAYMLER ELVRRTRFLP IAGATSSTYV EV LHLTQGT CWEQQYTPGG EAENDDLDQT LIIASRNIVR RSIVAIDPLA SLLSMCHTTS ISSEPLVEIL RSNPTDEQAV NIC KAALGI RINNSFSFGG YNFKRVKGSS QRTEKAVLTG NLQTLTMTIF EGYEEFNVSG KRASAVLKKG AQRLIQAIIG GRTL EDILN LMITLMVFSQ EEKMLKAVRG DLNFVNRANQ RLNPMYQLLR HFQKDSSTLL KNWGTEEIDP IMGIAGIMPD GTINK TQTL MGVRLSQGGV DEYSFNERIR VNIDKYLRVR NEKGELLISP EEVSEAQGQE KLPINYNSSL MWEVNGPESI LTNTYH WII KNWELLKTQW MTDPTVLYNR IEFEPFQTLI PKGNRAIYSG FTRTLFQQMR DVEGTFDSIQ IIKLLPFSAH PPSLGRT QF SSFTLNIRGA PLRLLIRGNS QVFNYNQMEN VIIVLGKSVG SPERSILTES SSIESAVLRG FLILGKANSK YGPVLTIG E LDKLGRGEKA NVLIGQGDTV LVMKRKRDSS ILTDSQTALK RIRLEESKGW SHPQFEKGGG SGGGSGGSAW SHPQFEKGR SGGENLYFQ UniProtKB: Polymerase basic protein 2 |
-Macromolecule #4: vRNA
Macromolecule | Name: vRNA / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.012289 KDa |
Sequence | String: AGUAGUAACA AGAGCAAUGU GUCCGUCUCG CCUCUGCUUC UGCU |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 31 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |