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- EMDB-45919: Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P -

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Basic information

Entry
Database: EMDB / ID: EMD-45919
TitleCryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P
Map data
Sample
  • Complex: M protein
    • Protein or peptide: short conformation Fab light chain
    • Protein or peptide: short conformation Fab heavy chain
    • Protein or peptide: Membrane protein
  • Ligand: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: POTASSIUM ION
KeywordsSARS-COV-2 / CORONAVIRUS / VIRAL PROTEIN / CAPSID PROTEIN / MEMBRANE PROTEIN
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: 3.03 Å
AuthorsDolan KA / Brohawn SG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI169896 United States
CitationJournal: bioRxiv / Year: 2024
Title: Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Authors: Mandira Dutta / Kimberly A Dolan / Souad Amiar / Elijah J Bass / Rokaia Sultana / Gregory A Voth / Stephen G Brohawn / Robert V Stahelin /
Abstract: M is the most abundant structural membrane protein in coronaviruses and is essential for the formation of infectious virus particles. SARS-CoV-2 M adopts two conformations, M and M, and regulated ...M is the most abundant structural membrane protein in coronaviruses and is essential for the formation of infectious virus particles. SARS-CoV-2 M adopts two conformations, M and M, and regulated transition between states is hypothesized to coordinate viral assembly and budding. However, the factors that regulate M conformation and roles for each state are unknown. Here, we discover a direct M-sphingolipid interaction that controls M conformational dynamics and virus assembly. We show M binds Golgi-enriched anionic lipids including ceramide-1-phosphate (C1P). Molecular dynamics simulations show C1P interaction promotes a long to short transition and energetically stabilizes M. Cryo-EM structures show C1P specifically binds M at a conserved site bridging transmembrane and cytoplasmic regions. Disrupting M-C1P interaction alters M subcellular localization, reduces interaction with Spike and E, and impairs subsequent virus-like particle cell entry. Together, these results show endogenous signaling lipids regulate M structure and support a model in which M is stabilized in the early endomembrane system to organize other structural proteins prior to viral budding.
History
DepositionJul 25, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45919.png

Downloads & links

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Map

FileDownload / File: emd_45919.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243.3 Å		0.81 Å/pix.
x 300 pix.
= 243.3 Å		0.81 Å/pix.
x 300 pix.
= 243.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.811 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.78185743 - 1.1466362
Average (Standard dev.)-0.000105404935 (±0.025913024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45919_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45919_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45919_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : M protein

EntireName: M protein
Components
  • Complex: M protein
    • Protein or peptide: short conformation Fab light chain
    • Protein or peptide: short conformation Fab heavy chain
    • Protein or peptide: Membrane protein
  • Ligand: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: POTASSIUM ION

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Supramolecule #1: M protein

SupramoleculeName: M protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 52 KDa

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Macromolecule #1: short conformation Fab light chain

MacromoleculeName: short conformation Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.220939 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLQTQVFIS LLLWISGAYG DIVMTQSPAS LAVSLGQRAT ISCKASQSID YDGDNYMNWY QQKPGQPPKL LIYTTSNLES GIPARFSGS GSGTDFTLNI HPVEEGDAAT YYCQQNNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MVLQTQVFIS LLLWISGAYG DIVMTQSPAS LAVSLGQRAT ISCKASQSID YDGDNYMNWY QQKPGQPPKL LIYTTSNLES GIPARFSGS GSGTDFTLNI HPVEEGDAAT YYCQQNNEDP YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #2: short conformation Fab heavy chain

MacromoleculeName: short conformation Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.779559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKHLWFFLLL VAAPRWVLSE VQLQQSGPEL VKPGASMKIS CKTSGYSFTG YTMNWVKQSH GKNLEWIGLI NPYNGDTSYN QKFKGKATL TVDKSSSTAY MELLSLTSED SAVYYCEVIN TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA QTNSMVTLGC L VKGYFPEP ...String:
MKHLWFFLLL VAAPRWVLSE VQLQQSGPEL VKPGASMKIS CKTSGYSFTG YTMNWVKQSH GKNLEWIGLI NPYNGDTSYN QKFKGKATL TVDKSSSTAY MELLSLTSED SAVYYCEVIN TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA QTNSMVTLGC L VKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRDCGCKP CI CTVPEVS SHHHHHHH

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Macromolecule #3: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 26.190693 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADSNGTITV EELKKLLEQW NLVIGFLFLT WICLLQFAYA NRNRFLYIIK LIFLWLLWPV TLACFVLAAV YRINWITGGI AIAMACLVG LMWLSYFIAS FRLFARTRSM WSFNPETNIL LNVPLHGTIL TRPLLESELV IGAVILRGHL RIAGHHLGRC D IKDLPKEI ...String:
MADSNGTITV EELKKLLEQW NLVIGFLFLT WICLLQFAYA NRNRFLYIIK LIFLWLLWPV TLACFVLAAV YRINWITGGI AIAMACLVG LMWLSYFIAS FRLFARTRSM WSFNPETNIL LNVPLHGTIL TRPLLESELV IGAVILRGHL RIAGHHLGRC D IKDLPKEI TVATSRTLSY YKLGASQRVA GDSGFAAYSR YRIGNYKLNT DHSSSSDNIA LLVQSNSLEV LFQ

UniProtKB: Membrane protein

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Macromolecule #4: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihyd...

MacromoleculeName: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 4 / Number of copies: 2 / Formula: 1PX
Molecular weightTheoretical: 617.881 Da
Chemical component information

ChemComp-1PX:
(2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKClPotassium Chloride
1.0 mM[CH2N(CH2CO2H)2]2Ethylenediaminetetraacetic acid
0.005 %C47H88O22Lauryl Maltose Neopentyl Glycol
0.0005 %C31H50O4Cholesteryl Hemisuccinate
100.0 uMC34H71N2O6PN-palmitoyl-ceramide-1-phosphate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ctk

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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