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- EMDB-35527: SARS-CoV-2,N protein -

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Basic information

Entry
Database: EMDB / ID: EMD-35527
TitleSARS-CoV-2,N protein
Map data
Sample
  • Complex: SARS-CoV-2 NFL and N182-419 protein assembly under physiological relevantl
KeywordsSARS-CoV-2 / N protein / PROTEIN FIBRIL / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsSu Z / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
CitationJournal: Mol Biomed / Year: 2023
Title: Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly.
Authors: Yan Wang / Xiaobin Ling / Chong Zhang / Jian Zou / Bingnan Luo / Yongbo Luo / Xinyu Jia / Guowen Jia / Minghua Zhang / Junchao Hu / Ting Liu / Yuanfeiyi Wang / Kefeng Lu / Dan Li / Jinbiao ...Authors: Yan Wang / Xiaobin Ling / Chong Zhang / Jian Zou / Bingnan Luo / Yongbo Luo / Xinyu Jia / Guowen Jia / Minghua Zhang / Junchao Hu / Ting Liu / Yuanfeiyi Wang / Kefeng Lu / Dan Li / Jinbiao Ma / Cong Liu / Zhaoming Su /
Abstract: SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA ...SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the N, the serine/arginine rich motif (SR), and the C. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (N) assembles into ring-like architecture whereas the truncated SR-CTD-C (N) promotes filamentous assembly. Moreover, LLPS droplets of N and N are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
History
DepositionMar 2, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35527.png

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Map

FileDownload / File: emd_35527.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.23 Å
Density
Contour LevelBy AUTHOR: 7.14
Minimum - Maximum-1.7376165 - 11.263617
Average (Standard dev.)0.71608 (±1.8030293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 452.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35527_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_35527_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 NFL and N182-419 protein assembly under physiological ...

EntireName: SARS-CoV-2 NFL and N182-419 protein assembly under physiological relevantl
Components
  • Complex: SARS-CoV-2 NFL and N182-419 protein assembly under physiological relevantl

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Supramolecule #1: SARS-CoV-2 NFL and N182-419 protein assembly under physiological ...

SupramoleculeName: SARS-CoV-2 NFL and N182-419 protein assembly under physiological relevantl
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranium acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1400
Image recordingFilm or detector model: OTHER / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2384
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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