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- EMDB-18945: 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat ... -
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Open data
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Basic information
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Title | 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide | ||||||||||||||||||||||||
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![]() | influenza / polymerase / PolII-CTD / VIRAL PROTEIN | ||||||||||||||||||||||||
Function / homology | ![]() 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / virus-mediated perturbation of host defense response / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | ||||||||||||||||||||||||
![]() | Keown JR / Carrique L / Fodor E / Grimes JM | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide Authors: Keown JR / Carrique L / Fodor E / Grimes JM | ||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 60 KB | ||
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() ![]() ![]() | 59.8 MB 59.5 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 834.2 KB | Display | ![]() |
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Full document | ![]() | 833.9 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r60MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened primary map
File | emd_18945_additional_1.map | ||||||||||||
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Annotation | Sharpened primary map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: deepEMhancer map produced with wideTarget and using the...
File | emd_18945_additional_2.map | ||||||||||||
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Annotation | deepEMhancer map produced with wideTarget and using the unsharpened map as the input (not half-maps) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map
File | emd_18945_half_map_1.map | ||||||||||||
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Annotation | half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map
File | emd_18945_half_map_2.map | ||||||||||||
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Annotation | half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 1918 H1N1 influenza virus heterotrimer in complex with a 4 repeat...
Entire | Name: 1918 H1N1 influenza virus heterotrimer in complex with a 4 repeat serine 5 phosphorylated peptide from PolII CTD |
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Components |
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-Supramolecule #1: 1918 H1N1 influenza virus heterotrimer in complex with a 4 repeat...
Supramolecule | Name: 1918 H1N1 influenza virus heterotrimer in complex with a 4 repeat serine 5 phosphorylated peptide from PolII CTD type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 82.663383 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINERGES IIVESGDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPAL YDYKENRFIE IGVTRREVHI YYLEKANKIK SEKTHIHIFS FTGEEMATKA D YTLDEESR ...String: MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINERGES IIVESGDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPAL YDYKENRFIE IGVTRREVHI YYLEKANKIK SEKTHIHIFS FTGEEMATKA D YTLDEESR ARIKTRLFTI RQEMASRGLW DSFRQSERGE ETIEERFEIT GTMRRLADQS LPPNFSSLEN FRAYVDGFEP NG YIEGKLS QMSKEVNARI EPFLKTTPRP LRLPDGPPCS QRSKFLLMDA LKLSIEDPSH EGEGIPLYDA IKCMRTFFGW KEP NVVKPH EKGINPNYLL AWKQVLAELQ DIENEEKIPK TKNMKKTSQL KWALGENMAP EKVDFDDCKD VSDLKQYDSD EPEL RSLAS WIQSEFNKAC ELTDSSWIEL DEIGEDVAPI EHIASMRRNY FTAEVSHCRA TEYIMKGVYI NTALLNASCA AMDDF QLIP MISKCRTKEG RRKTNLYGFI IKGRSHLRND TDVVNFVSME FSLTDPRLEP HKWEKYCVLE IGDMLLRSAI GQVSRP MFL YVRTNGTSKI KMKWGMEMRR CLLQSLQQIE SMIEAESSVK EKDMTKEFFE NKSETWPIGE SPKGVEEGSI GKVCRTL LA KSVFNSLYAS PQLEGFSAES RKLLLIVQAL RDNLEPGTFD LGGLYEAIEE CLINDPWVLL NASWFNSFLT HALR UniProtKB: Polymerase acidic protein |
-Macromolecule #2: Polymerase basic protein 2
Macromolecule | Name: Polymerase basic protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 102.377219 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQGQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSAV HYPKIYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF ...String: MERIKELRDL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPALRMKWM MAMKYPITAD KRIMEMIPER NEQGQTLWSK TNDAGSDRV MVSPLAVTWW NRNGPTTSAV HYPKIYKTYF EKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF PNEVGARILT SESQLTITKE KKEELQDCKI SPLMVAYMLE RELVRKTRFL PVAGGTSSVY IEVLHLTQGT CW EQMYTPG GEVRNDDVDQ SLIIAARNIV RRATVSADPL ASLLEMCHST QIGGIRMVDI LRQNPTEEQA VDICKAAMGL RIS SSFSFG GFTFKRTSGS SVKREEEVLT GNLQTLKIRV HEGYEEFTMV GRRATAILRK ATRRLIQLIV SGRDEQSIAE AIIV AMVFS QEDCMIKAVR GDLNFVNRAN QRLNPMHQLL RHFQKDAKVL FQNWGIEPID NVMGMIGILP DMTPSTEMSM RGVRV SKMG VDEYSSTERV VVSIDRFLRV RDQRGNVLLS PEEVSETQGT EKLTITYSSS MMWEVNGPES VLVNTYQWII RNWETV KIQ WSQNPTMLYN KMEFEPFQSL VPKAARGQYS GFVRTLFQQM RDVLGTFDTV QIIKLLPFAA APPKQSRMQF SSLTVNV RG SGMRILVRGN SPVFNYNKAT KRLTVLGKDA GALTEDPDEG TAGVESAVLR GFLILGKEDR RYGPALSINE LSNLAKGE K ANVLIGQGDV VLVMKRKRDS SILTDSQTAT KRIRMAINEN LYFQGELKTA ALAQHDEAVD NKFNKEQQNA FYEILHLPN LNEEQRNAFI QSLKDDPSQS ANLLAEAKKL NDAQAPKVDN KFNKEQQNAF YEILHLPNLN EEQRNAFIQS LKADPSQSAN LLAEAKKLN GAQAPKVDAN SAGKST UniProtKB: Polymerase basic protein 2 |
-Macromolecule #5: RNA polymerase II 4 repeat peptide with serine5 phosphorylation
Macromolecule | Name: RNA polymerase II 4 repeat peptide with serine5 phosphorylation type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.216893 KDa |
Sequence | String: YSPT(SEP)PSYSP T(SEP)PSYSPT(SEP)P SYSPT(SEP)PS |
-Macromolecule #6: RNA-directed RNA polymerase catalytic subunit
Macromolecule | Name: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 86.625211 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGRWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK ...String: MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGRWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DKLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK DVMESMDKEE MEITTHFQRK RRVRDNMTKK MVTQRTIGKK KQRLNKRSYL IRALTLNTMT KDAERGKLKR RA IATPGMQ IRGFVYFVET LARSICEKLE QSGLPVGGNE KKAKLANVVR KMMTNSQDTE LSFTITGDNT KWNENQNPRM FLA MITYIT RNQPEWFRNV LSIAPIMFSN KMARLGKGYM FESKSMKLRT QIPAEMLASI DLKYFNDSTR KKIEKIRPLL IDGT ASLSP GMMMGMFNML STVLGVSILN LGQKRYTKTT YWWDGLQSSD DFALIVNAPN HEGIQAGVDR FYRTCKLLGI NMSKK KSYI NRTGTFEFTS FFYRYGFVAN FSMELPSFGV SGINESADMS IGVTVIKNNM INNDLGPATA QMALQLFIKD YRYTYR CHR GDTQIQTRRS FEIKKLWEQT RSKAGLLVSD GGPNLYNIRN LHIPEVCLKW ELMDEDYQGR LCNPLNPFVS HKEIESV NN AVMMPAHGPA KNMEYDAVAT THSWIPKRNR SILNTSQRGI LEDEQMYQKC CNLFEKFFPS SSYRRPVGIS SMVEAMVS R ARIDARIDFE SGRIKKEEFA EIMKICSTIE ELRRQK UniProtKB: RNA-directed RNA polymerase catalytic subunit |
-Macromolecule #3: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3')
Macromolecule | Name: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.862017 KDa |
Sequence | String: AGUAGAAACA AGGCC |
-Macromolecule #4: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3')
Macromolecule | Name: RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 5.335125 KDa |
Sequence | String: GGCCUGCUUU UGCUAUU |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Rigid body fit of the polymerase heterotrimer 7NHX followed by model building of the PolII peptide |
Refinement | Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8r60: |