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- EMDB-31978: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-31978
TitleSARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Map data
Sample
  • Complex: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
    • Complex: Membrane protein
      • Protein or peptide: Membrane protein
    • Complex: YN7717_9 Fab
      • Protein or peptide: YN7717_9 Fab light chain
      • Protein or peptide: YN7717_9 Fab heavy chain
KeywordsSARS-CoV-2 / M protein / viral structural protein / virus assembly / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of protein M / SARS-CoV-2 modulates autophagy / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / VEGFR2 mediated vascular permeability / PIP3 activates AKT signaling / TRAF3-dependent IRF activation pathway ...Maturation of protein M / SARS-CoV-2 modulates autophagy / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / VEGFR2 mediated vascular permeability / PIP3 activates AKT signaling / TRAF3-dependent IRF activation pathway / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / viral envelope / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile.
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31978.png

Downloads & links

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Map

FileDownload / File: emd_31978.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 Å		1.25 Å/pix.
x 240 pix.
= 298.8 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: 0.75
Minimum - Maximum-2.1254354 - 4.7288294
Average (Standard dev.)0.0034841727 (±0.099605165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 298.8 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 (short form) in complex with YN7717_9 Fab

EntireName: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Components
  • Complex: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
    • Complex: Membrane protein
      • Protein or peptide: Membrane protein
    • Complex: YN7717_9 Fab
      • Protein or peptide: YN7717_9 Fab light chain
      • Protein or peptide: YN7717_9 Fab heavy chain

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Supramolecule #1: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab

SupramoleculeName: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Membrane protein

SupramoleculeName: Membrane protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: YN7717_9 Fab

SupramoleculeName: YN7717_9 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 28.257822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHD YKDDDDKENL YFQGMADSNG TITVEELKKL LEQWNLVIGF LFLTWICLLQ FAYANRNRFL YIIKLIFLWL LWPVTLACF VLAAVYRINW ITGGIAIAMA CLVGLMWLSY FIASFRLFAR TRSMWSFNPE TNILLNVPLH GTILTRPLLE S ELVIGAVI ...String:
MHHHHHHHHD YKDDDDKENL YFQGMADSNG TITVEELKKL LEQWNLVIGF LFLTWICLLQ FAYANRNRFL YIIKLIFLWL LWPVTLACF VLAAVYRINW ITGGIAIAMA CLVGLMWLSY FIASFRLFAR TRSMWSFNPE TNILLNVPLH GTILTRPLLE S ELVIGAVI LRGHLRIAGH HLGRCDIKDL PKEITVATSR TLSYYKLGAS QRVAGDSGFA AYSRYRIGNY KLNTDHSSSS DN IALLVQ

UniProtKB: Membrane protein

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Macromolecule #2: YN7717_9 Fab light chain

MacromoleculeName: YN7717_9 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.999266 KDa
SequenceString: DIVMTQSPAS LAVSLGQRAT ISCKASQSID YDGDNYMNWY QQKPGQPPKL LIYTTSNLES GIPARFSGSG SGTDFTLNIH PVEEGDAAT YYCQQNNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVMTQSPAS LAVSLGQRAT ISCKASQSID YDGDNYMNWY QQKPGQPPKL LIYTTSNLES GIPARFSGSG SGTDFTLNIH PVEEGDAAT YYCQQNNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #3: YN7717_9 Fab heavy chain

MacromoleculeName: YN7717_9 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.499639 KDa
SequenceString: EVQLQQSGPE LVKPGASMKI SCKTSGYSFT GYTMNWVKQS HGKNLEWIGL INPYNGDTSY NQKFKGKATL TVDKSSSTAY MELLSLTSE DSAVYYCEVI NTYWGQGTLV TVSAAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL S SGVHTFPA ...String:
EVQLQQSGPE LVKPGASMKI SCKTSGYSFT GYTMNWVKQS HGKNLEWIGL INPYNGDTSY NQKFKGKATL TVDKSSSTAY MELLSLTSE DSAVYYCEVI NTYWGQGTLV TVSAAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL S SGVHTFPA VLQSDLYTLS SSVTVPSSTW PSETVTCNVA HPASSTKVDK KIVPRDCGCK PCICTVPEVS S

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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

Concentration1.5 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.4 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

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22011
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7vgs:
SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab

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