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Yorodumi- EMDB-19599: Structural characterization of Thogoto Virus nucleoprotein provid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19599 | |||||||||
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Title | Structural characterization of Thogoto Virus nucleoprotein provides insights into RNA encapsidation and assembly | |||||||||
Map data | filtered to 18A, non-sharpened | |||||||||
Sample |
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Keywords | Viral replication / nucleoprotein / RNA binding / oligomerization / orthomyxovirus / VIRAL PROTEIN | |||||||||
Function / homology | helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / RNA binding / Nucleoprotein Function and homology information | |||||||||
Biological species | Thogotovirus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Roske Y / Mikirtumov V / Daumke O / Kudryashev M / Dick A | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Structure / Year: 2024 Title: Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly. Authors: Alexej Dick / Vasilii Mikirtumov / Jonas Fuchs / Ferdinand Krupp / Daniel Olal / Elias Bendl / Thiemo Sprink / Christoph Diebolder / Mikhail Kudryashev / Georg Kochs / Yvette Roske / Oliver Daumke / Abstract: Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ...Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ribonucleoprotein complexes (RNPs). NP structures of several influenza viruses have been reported. However, there are still contradictory models of how orthomyxovirus RNPs are assembled. Here, we characterize the crystal structure of Thogoto virus (THOV) NP and found striking similarities to structures of influenza viral NPs, including a two-lobed domain architecture, a positively charged RNA-binding cleft, and a tail loop important for trimerization and viral transcription. A low-resolution cryo-electron tomography reconstruction of THOV RNPs elucidates a left-handed double helical assembly. By providing a model for RNP assembly of THOV, our study suggests conserved NP assembly and RNA encapsidation modes for thogoto- and influenza viruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19599.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-19599-v30.xml emd-19599.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19599_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_19599.png | 67.1 KB | ||
Masks | emd_19599_msk_1.map | 27 MB | Mask map | |
Filedesc metadata | emd-19599.cif.gz | 5.6 KB | ||
Others | emd_19599_half_map_1.map.gz emd_19599_half_map_2.map.gz | 13.3 MB 13.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19599 | HTTPS FTP |
-Validation report
Summary document | emd_19599_validation.pdf.gz | 946.9 KB | Display | EMDB validaton report |
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Full document | emd_19599_full_validation.pdf.gz | 946.4 KB | Display | |
Data in XML | emd_19599_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_19599_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19599 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19599 | HTTPS FTP |
-Related structure data
Related structure data | 8rytMC 8cjwC 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_19599.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | filtered to 18A, non-sharpened | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.6 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19599_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19599_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19599_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ribonucleoprotein (RNP) complexes of Thogoto virus
Entire | Name: Ribonucleoprotein (RNP) complexes of Thogoto virus |
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Components |
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-Supramolecule #1: Ribonucleoprotein (RNP) complexes of Thogoto virus
Supramolecule | Name: Ribonucleoprotein (RNP) complexes of Thogoto virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thogotovirus |
-Macromolecule #1: THOV RNP
Macromolecule | Name: THOV RNP / type: other / ID: 1 / Details: Nucleoprotein / Classification: other |
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Source (natural) | Organism: Thogotovirus / Strain: THOV strain SiAr 126 |
Sequence | String: MATDQMDISG PPPKKQHVDT ESQIPKMYEM IRDQMRTLAS THKIPLNIDH NCEVIGSIIM AACTNNRDLR PVDKYWFLMG PAGAEVMTEV EIDIQPQLQW AKGAVHDPKY KGQWYPFLAL LQISNKTKDT ILWQKYPVTQ ELEISNSLEI YANGHGIKDR LKNSRPRSVG ...String: MATDQMDISG PPPKKQHVDT ESQIPKMYEM IRDQMRTLAS THKIPLNIDH NCEVIGSIIM AACTNNRDLR PVDKYWFLMG PAGAEVMTEV EIDIQPQLQW AKGAVHDPKY KGQWYPFLAL LQISNKTKDT ILWQKYPVTQ ELEISNSLEI YANGHGIKDR LKNSRPRSVG PLVHLLHLKR LQENPPKSPA VNGIRKSIVG HLKRQCIGET QKAMINQFEM GRWESLSTFA ASLLAIKPRI ENHFVLTYPL IANCEDFAGA TLSDEWVFKA MEKISNKKTL RVCGPDEKWI SFMNQIYIHS VFQTTGEDLG VLEWVFGGRF CQRKEFGRYC KKSQTKVIGL FTFQYEYWSK PLKSAPRSIE GSKRGQISCR PSFKGKRPSY NNFTSIDALQ SASGSQTVSF YDQVREECQK YMDLKVEGTT CFYRKGGHVE VEFPGSAHCN TYLFG |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 1 / Average exposure time: 1.2 sec. / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 5.0 µm / Calibrated defocus min: 3.0 µm / Calibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |