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Yorodumi- EMDB-17333: Thogoto virus polymerase in Mode A conformation and bound to 35-m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17333 | |||||||||
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Title | Thogoto virus polymerase in Mode A conformation and bound to 35-mer loop promoter RNA | |||||||||
Map data | LocScale filtered | |||||||||
Sample |
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Keywords | Thogoto / viral RNA-dependent RNA polymerase / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information cap snatching / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / host cell nucleus / RNA binding Similarity search - Function | |||||||||
Biological species | Thogotovirus thogotoense | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Cusack S / Kouba T | |||||||||
Funding support | France, 1 items
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Citation | Journal: To Be Published Title: Thogoto virus polymerase Authors: Kouba T / Cusack S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17333.map.gz | 61.7 MB | EMDB map data format | |
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Header (meta data) | emd-17333-v30.xml emd-17333.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17333_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_17333.png | 92.7 KB | ||
Masks | emd_17333_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17333.cif.gz | 6.9 KB | ||
Others | emd_17333_additional_1.map.gz emd_17333_half_map_1.map.gz emd_17333_half_map_2.map.gz | 117.1 MB 98.6 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17333 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17333 | HTTPS FTP |
-Related structure data
Related structure data | 8p0gMC 8p0bC 8p0uC 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_17333.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | LocScale filtered | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17333_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: RELION post-processed
File | emd_17333_additional_1.map | ||||||||||||
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Annotation | RELION post-processed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17333_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17333_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Thogotovirus RNA-directed RNA polymerase
Entire | Name: Thogotovirus RNA-directed RNA polymerase |
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Components |
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-Supramolecule #1: Thogotovirus RNA-directed RNA polymerase
Supramolecule | Name: Thogotovirus RNA-directed RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Thogotovirus thogotoense |
Molecular weight | Theoretical: 240 KDa |
-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: Thogotovirus thogotoense |
Molecular weight | Theoretical: 71.551383 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MTDRPDHIDS RVWELSETQE DWITQVHGHV RRVVECWKYT ICCLISNMHT HRGAPQYDVF KWQDRSTIEW ICSKKKVQYP ERDTPDLYD NERAVAYKVL LVSDLSDHSP TSGIYHDLAF NLEGEAEESC ALVLRGSQLQ DIKGFLCRAL EWVVSNNLTQ E VVETISGE ...String: MTDRPDHIDS RVWELSETQE DWITQVHGHV RRVVECWKYT ICCLISNMHT HRGAPQYDVF KWQDRSTIEW ICSKKKVQYP ERDTPDLYD NERAVAYKVL LVSDLSDHSP TSGIYHDLAF NLEGEAEESC ALVLRGSQLQ DIKGFLCRAL EWVVSNNLTQ E VVETISGE AKLQFSVGTT FRTLLKRDTD WDVIPTPRVE PNVPRIEGRR WTQMKKLPLL KEKEGPPSPW RALLLGADSE YI VCPPGTD QEAISWIHSQ SEIECIRESK STPASVITCL TSSLQSFAEG NPVRSRIHED IIAFGINKKQ EKKQSASSSA SGE WKRAEY QVEEMSLPPW VEEEMVLLRS DQEDNWIELE KNAIYTEVDG VAEGLVDKYI EIVGRTKVAS VIEKWQIAAT RTFS QLHTD RSRITACPII TRDPSGNCQF WGMVLLGPHH VKRDTDNAPL LIAEIMGEDT EEKYPKHSVF SLKVEGKQFL LSLKI TSFS RNKLYTFSNI RRVLIQPASI YSQVVLSRAA ENNSLNLEVN PEIQLYLEGA QRGMTLYQWV RMILCLEFLM AIYNNP QME GFLANMRRLH MSRHAMMERR QVFLPFGSRP EDKVNECIIN NPIVAYLAKG WNSMPNVYY 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: Thogotovirus thogotoense |
Molecular weight | Theoretical: 81.476703 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNLFTPRSEI NPTTTQELLY AYTGPAPVAY GTRTRAVLEN IIRPYQYFYK EPNVQRALDI KTGCKEPEDI NVEGPSSGFH TASVLKLAD NFFRKYRPAM EKLKYWILVK LPKLKYAELS KGRQTYSFIH KRNLPAPIAL EETVEFLEQN LRRKIGPTLL S YCQAIADV ...String: MNLFTPRSEI NPTTTQELLY AYTGPAPVAY GTRTRAVLEN IIRPYQYFYK EPNVQRALDI KTGCKEPEDI NVEGPSSGFH TASVLKLAD NFFRKYRPAM EKLKYWILVK LPKLKYAELS KGRQTYSFIH KRNLPAPIAL EETVEFLEQN LRRKIGPTLL S YCQAIADV MELDETTYEG ARDPRPWDIQ LEEIDSDEED PLFRQVGREE TYTIKFSREE LWDQMRTLNT MWKHLERGRL NR RTIATPS MLIRGFVKIV EDAAKEILEN VPTSGVPVGG EEKLAKLASK QTFHTAVTGE LSGDQEKFNE CLDPDAMRLM WTV FLRKLG CPDWIMELFN IPFMVFKSKL ADMGEGLVYT KGKLTDRKPL GEMPSEFDDL VRNVVGNSIS CRLGMFMGMY NLTS TLLAL ISIEREELTG SHVESSDDFI HFFNCKTHEE MFKQAETLRL TLKLVGINMS PSKCILISPA GIGEFNSKFH HRDFV GNVA TELPALVPNG TNPMTDLAMG LNVIKHSVNT GQMNLCTGAL AMRIFNHAYK YAYMALGVTR RTRFMEENAI TPLLTN QGA SPVHSFSTMH LDEVALRRHL GLLDEETLRR ILNPNNPVTQ KGDPSMFFRI ENKMPQIMED YSVPSCFKYT LSRNRTI QD KPHKALLNKE ERYQRVTSII NKLFPEVLIQ EASAPGTVRE SLKRRLELVV ERSDLDEERK KRILSRIF 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: Thogotovirus thogotoense |
Molecular weight | Theoretical: 88.172953 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDREEPAESE CTLRALVEEY NGACKEAPKE MSKQFTDYNT FKRYTTSKKD HAPQMRLVYS VRKPWPISMT PSKEIPLVFN GTKLKDTIL DLGESKRTRA NIVVPDYWSK YGSQTSLEVV NAILYAEDLK VQRFFSTEWG EIRYGRMLPF RKPVQACPTI E EVNPASIP ...String: MDREEPAESE CTLRALVEEY NGACKEAPKE MSKQFTDYNT FKRYTTSKKD HAPQMRLVYS VRKPWPISMT PSKEIPLVFN GTKLKDTIL DLGESKRTRA NIVVPDYWSK YGSQTSLEVV NAILYAEDLK VQRFFSTEWG EIRYGRMLPF RKPVQACPTI E EVNPASIP HTLLQVFCPQ YTTLDSKRKA HMGAVEKLKR VMEPICKVQT QESAVHIARS LIDSNKKWLP TVVDHTPRTA EM AHFLCSK YHYVHTNTQD LSDTRSIDNL CGELVKRSLK CRCPKETLVA NLDKITIQGR PMREVLADHD GELPYLGICR VAM GLSTHH TMKIRSTKFS ILNSDHPRIE VKKVFSLSPD VQVTIPYRRF KGKAKVYFQN DQIQGYFSCT DRQIDEIKIS APKN APLLE PLLDICYYGS FIEPGFEQTF GFYPAGKREF VDSFFMHHSK DHKAFLIHMG LDKDLSLPLS PELNWKEPAL SKVCR VTEL DSTVQPYTSA TREFVLGETL NVYTQHENGL ELLICPTEIR STRGPLPPGT NLSGSEFIDI YQDPFSRAKS LLKSTI LHA ERCKEFVGNM LEEYQDPAET TVQSLVPINT WGKSAKRKLQ EEITSDPDWH QCPRKRAKMS YLAIIAGSIQ DRDKKQT NV PRAFMLRGSQ IEYDMKATRG LVVDTTNRII VGGETVLREG KGGPEGYVQT GVFEEQPRCY LVDTPDHGLS MGLSRFCV H SQGRYFQYEK KISIWEETDN IKATIDSQRD LKRRRDIEEM VSKRARIV UniProtKB: Polymerase basic protein 2 |
-Macromolecule #4: 5'RNA
Macromolecule | Name: 5'RNA / type: rna / ID: 4 / Number of copies: 2 |
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Source (natural) | Organism: Thogotovirus thogotoense |
Molecular weight | Theoretical: 11.158626 KDa |
Sequence | String: AGAGAAAUCA AGGCCCCCGG CCUGUUUUUG CUAUU |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / 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
Buffer | pH: 8 |
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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 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |