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- EMDB-31976: Cryo-EM reconstruction of SARS-CoV-2 M protein dimer in LMNG/CHS ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31976
TitleCryo-EM reconstruction of SARS-CoV-2 M protein dimer in LMNG/CHS micelle
Map data
Sample
  • Complex: SARS-CoV-2 M protein dimer in LMNG/CHS micelle
KeywordsSARS-CoV-2 / M protein / viral structural protein / virus assembly / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsZhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structure of SARS-CoV-2 membrane protein essential for virus assembly.
Authors: Zhikuan Zhang / Norimichi Nomura / Yukiko Muramoto / Toru Ekimoto / Tomoko Uemura / Kehong Liu / Moeko Yui / Nozomu Kono / Junken Aoki / Mitsunori Ikeguchi / Takeshi Noda / So Iwata / ...Authors: Zhikuan Zhang / Norimichi Nomura / Yukiko Muramoto / Toru Ekimoto / Tomoko Uemura / Kehong Liu / Moeko Yui / Nozomu Kono / Junken Aoki / Mitsunori Ikeguchi / Takeshi Noda / So Iwata / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus ...The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein.
History
DepositionSep 18, 2021-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31976.png

Downloads & links

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Map

FileDownload / File: emd_31976.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.337
Minimum - Maximum-0.3803702 - 1.1473148
Average (Standard dev.)0.00043817202 (±0.047699187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 M protein dimer in LMNG/CHS micelle

EntireName: SARS-CoV-2 M protein dimer in LMNG/CHS micelle
Components
  • Complex: SARS-CoV-2 M protein dimer in LMNG/CHS micelle

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Supramolecule #1: SARS-CoV-2 M protein dimer in LMNG/CHS micelle

SupramoleculeName: SARS-CoV-2 M protein dimer in LMNG/CHS micelle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 348142
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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