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Yorodumi- EMDB-12918: Cryo-EM structure of the Cetacean morbillivirus nucleoprotein-RNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12918 | |||||||||
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Title | Cryo-EM structure of the Cetacean morbillivirus nucleoprotein-RNA complex | |||||||||
Map data | Masked postprocessed map | |||||||||
Sample |
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Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / Nucleocapsid Function and homology information | |||||||||
Biological species | Morbillivirus sp. | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Zinzula L / Beck F / Klumpe S / Bohn S / Pfeifer G / Bollschweiler D / Nagy I / Plitzko JM / Baumeister W | |||||||||
Citation | Journal: J Struct Biol / Year: 2021 Title: Cryo-EM structure of the cetacean morbillivirus nucleoprotein-RNA complex. Authors: Luca Zinzula / Florian Beck / Sven Klumpe / Stefan Bohn / Günter Pfeifer / Daniel Bollschweiler / István Nagy / Jürgen M Plitzko / Wolfgang Baumeister / Abstract: Cetacean morbillivirus (CeMV) is an emerging and highly infectious paramyxovirus that causes outbreaks in cetaceans and occasionally in pinnipeds, representing a major threat to biodiversity and ...Cetacean morbillivirus (CeMV) is an emerging and highly infectious paramyxovirus that causes outbreaks in cetaceans and occasionally in pinnipeds, representing a major threat to biodiversity and conservation of endangered marine mammal populations in both hemispheres. As for all non-segmented, negative-sense, single-stranded RNA (ssRNA) viruses, the morbilliviral genome is enwrapped by thousands of nucleoprotein (N) protomers. Each bound to six ribonucleotides, N protomers assemble to form a helical ribonucleoprotein (RNP) complex that serves as scaffold for nucleocapsid formation and as template for viral replication and transcription. While the molecular details on RNP complexes elucidated in human measles virus (MeV) served as paradigm model for these processes in all members of the Morbillivirus genus, no structural information has been obtained from other morbilliviruses, nor has any CeMV structure been solved so far. We report the structure of the CeMV RNP complex, reconstituted in vitro upon binding of recombinant CeMV N to poly-adenine ssRNA hexamers and solved to 4.0 Å resolution by cryo-electron microscopy. In spite of the amino acid sequence similarity and consequently similar folding of the N protomer, the CeMV RNP complex exhibits different helical parameters as compared to previously reported MeV orthologs. The CeMV structure reveals exclusive interactions leading to more extensive protomer-RNA and protomer-protomer interfaces. We identified twelve residues, among those varying between CeMV strains, as putatively important for the stabilization of the RNP complex, which highlights the need to study the potential of CeMV N mutations that modulate nucleocapsid assembly to also affect viral phenotype and host adaptation. | |||||||||
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_12918.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-12918-v30.xml emd-12918.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12918_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_12918.png | 162.6 KB | ||
Masks | emd_12918_msk_1.map | 64 MB | Mask map | |
Others | emd_12918_additional_1.map.gz emd_12918_additional_2.map.gz emd_12918_half_map_1.map.gz emd_12918_half_map_2.map.gz | 56.3 MB 49.5 MB 49.7 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12918 | HTTPS FTP |
-Related structure data
Related structure data | 7oi3MC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12918.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Masked postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12918_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: DeepEMhancer map
File | emd_12918_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer map | ||||||||||||
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Density Histograms |
-Additional map: Map before postprocessing
File | emd_12918_additional_2.map | ||||||||||||
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Annotation | Map before postprocessing | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_12918_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_12918_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cetacean morbillivirus nucleoprotein-RNA complex
Entire | Name: Cetacean morbillivirus nucleoprotein-RNA complex |
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Components |
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-Supramolecule #1: Cetacean morbillivirus nucleoprotein-RNA complex
Supramolecule | Name: Cetacean morbillivirus nucleoprotein-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Cetacean morbillivirus nucleoprotein
Supramolecule | Name: Cetacean morbillivirus nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Morbillivirus sp. |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Supramolecule #3: poly-A 6-mer
Supramolecule | Name: poly-A 6-mer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Morbillivirus sp. |
Recombinant expression | Organism: Synthetic construct (others) |
-Macromolecule #1: Cetacean morbillivirus nucleoprotein
Macromolecule | Name: Cetacean morbillivirus nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Morbillivirus sp. |
Molecular weight | Theoretical: 46.273625 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GMATLLRSLA LFKRNKDRTP LTAGSGGAIR GIKHVIVVPV PGDSSIVTRS RLLDRLVRLA GDPYISGPKL TGVMISILSL FVESPSQLI QRITDDPDVS IRLVEVIQSE KSLSGLTFAS RGANMEDEAD DYFSIQAGEE GDTRGTHWFE NKEIVEIEVQ D PEEFNILL ...String: GMATLLRSLA LFKRNKDRTP LTAGSGGAIR GIKHVIVVPV PGDSSIVTRS RLLDRLVRLA GDPYISGPKL TGVMISILSL FVESPSQLI QRITDDPDVS IRLVEVIQSE KSLSGLTFAS RGANMEDEAD DYFSIQAGEE GDTRGTHWFE NKEIVEIEVQ D PEEFNILL ASILAQIWIL LAKAVTAPDT AADSETRRWI KYTQQRRVVG EFRLDKGWLD AVRNRIAEDL SLRRFMVALI LD IKRTPGN KPRIAEMICD IDTYIVEAGL ASFILTIKFG IETMYPALGL HEFSGELTTV ESLMNLYQQM GETAPYMVIL ENS IQNKFS AGSYPLLWSY AMGVGVELEN SMGGLNFGRS YFDPAYFRLG QEMVRRSAGK VSSSLAAELG ITAEDAKLVS EIAA QANDD RVEHHHHHHH H |
-Macromolecule #2: poly-A 6-mer
Macromolecule | Name: poly-A 6-mer / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Morbillivirus sp. |
Molecular weight | Theoretical: 1.930277 KDa |
Sequence | String: AAAAAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.8 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3153 / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |