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- PDB-7vgr: SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab -

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Basic information

Entry
Database: PDB / ID: 7vgr
TitleSARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab
Components
  • Membrane protein
  • YN7756_1 Fab heavy chain
  • YN7756_1 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhang, Z. / Ohto, U. / Shimizu, T.
Funding support1items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.0Aug 3, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 3, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Aug 3, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 3, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 3, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 3, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
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Revision 1.3Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: YN7756_1 Fab light chain
D: YN7756_1 Fab heavy chain
E: YN7756_1 Fab light chain
F: YN7756_1 Fab heavy chain
A: Membrane protein
B: Membrane protein


Theoretical massNumber of molelcules
Total (without water)154,7956
Polymers154,7956
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17410 Å2
ΔGint-128 kcal/mol
Surface area55940 Å2

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Components

#1: Antibody YN7756_1 Fab light chain


Mass: 24025.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody YN7756_1 Fab heavy chain


Mass: 25114.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Membrane protein / M / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


Mass: 28257.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: P0DTC5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 FabCOMPLEXall0MULTIPLE SOURCES
2YN7756_1 FabCOMPLEX#1-#21NATURAL
3Membrane proteinCOMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mus musculus (house mouse)10090
33Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 61.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263166 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210134
ELECTRON MICROSCOPYf_angle_d0.52813830
ELECTRON MICROSCOPYf_dihedral_angle_d3.1471406
ELECTRON MICROSCOPYf_chiral_restr0.041570
ELECTRON MICROSCOPYf_plane_restr0.0041742

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