|Entry||Database: EMDB / ID: 0333|
|Title||Helical RNA-bound Hantaan virus nucleocapsid|
|Map data||Helical RNA-bound Hantaan virus nucleocapsid structure|
|Sample||RNA-bound Hantaan virus nucleocapsid:|
Hantaan virus nucleoprotein / RNA / nucleic-acidNucleic acid / Nucleoprotein
|Function / homology||Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / RNA binding / Nucleoprotein|
Function and homology information
|Source||Hantaan orthohantavirus / Spodoptera frugiperda (fall armyworm) / Fall armyworm (fall armyworm)|
|Method||helical reconstruction / cryo EM / 3.3 Å resolution|
|Authors||Arragain B / Reguera J / Desfosses A / Gutsche I / Schoehn G / Malet H|
|Citation||Journal: Elife / Year: 2019|
Title: High resolution cryo-EM structure of the helical RNA-bound Hantaan virus nucleocapsid reveals its assembly mechanisms.
Authors: Benoît Arragain / Juan Reguera / Ambroise Desfosses / Irina Gutsche / Guy Schoehn / Hélène Malet
Abstract: Negative-strand RNA viruses condense their genome into helical nucleocapsids that constitute essential templates for viral replication and transcription. The intrinsic flexibility of nucleocapsids ...Negative-strand RNA viruses condense their genome into helical nucleocapsids that constitute essential templates for viral replication and transcription. The intrinsic flexibility of nucleocapsids usually prevents their full-length structural characterisation at high resolution. Here, we describe purification of full-length recombinant metastable helical nucleocapsid of Hantaan virus ( family, order) and determine its structure at 3.3 Å resolution by cryo-electron microscopy. The structure reveals the mechanisms of helical multimerisation via sub-domain exchanges between protomers and highlights nucleotide positions in a continuous positively charged groove compatible with viral genome binding. It uncovers key sites for future structure-based design of antivirals that are currently lacking to counteract life-threatening hantavirus infections. The structure also suggests a model of nucleoprotein-polymerase interaction that would enable replication and transcription solely upon local disruption of the nucleocapsid.
|Validation Report||PDB-ID: 6i2n|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 1, 2018 / Header (metadata) release: Dec 19, 2018 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_0333.map.gz (map file in CCP4 format, 256001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.067 Å|
CCP4 map header:
+Entire RNA-bound Hantaan virus nucleocapsid
|Entire||Name: RNA-bound Hantaan virus nucleocapsid / Number of components: 5|
+Component #1: protein, RNA-bound Hantaan virus nucleocapsid
|Protein||Name: RNA-bound Hantaan virus nucleocapsid / Recombinant expression: No|
|Mass||Theoretical: 48.2 kDa|
+Component #2: protein, Hantaan virus nucleoprotein
|Protein||Name: Hantaan virus nucleoprotein / Recombinant expression: No|
|Source||Species: Hantaan orthohantavirus|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFastBac / Strain: SF21|
+Component #3: protein, RNA
|Protein||Name: RNA / Recombinant expression: No|
|Source||Species: Spodoptera frugiperda (fall armyworm)|
+Component #4: nucleic-acid, RNA (5'-R(P*UP*UP*U)-3')
|Nucleic-acid||Name: RNA (5'-R(P*UP*UP*U)-3') / Class: RNA|
Details: A poly-U has been built but the RNA corresponds to heterogeneous insect cell RNA that bind to nucleoproteins during expression.
Structure: OTHER / Synthetic: No
|Mass||Theoretical: 0.87354 kDa|
|Source||Species: Fall armyworm (fall armyworm)|
+Component #5: protein, Nucleoprotein
|Protein||Name: Nucleoprotein / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 48.262266 kDa|
|Source||Species: Hantaan orthohantavirus|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 18.87 Å / Delta phi: -99.95 deg.|
|Sample solution||Specimen conc.: 0.6 mg/ml / pH: 8|
|Support film||30 mA|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %|
Details: 3 ul of sample were applied on the resulting glow-discharged grids and excess solution was blotted during 2.5 sec force 7.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 46860.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 4328 / Sampling size: 5 microns|
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