+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26993 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 M protein in a lipid nanodisc | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-COV-2 / CORONAVIRUS / VIRAL PROTEIN / CAPSID PROTEIN / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / endoplasmic reticulum-Golgi intermediate compartment / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / VEGFR2 mediated vascular permeability ...Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / endoplasmic reticulum-Golgi intermediate compartment / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / virus-mediated perturbation of host defense response / viral envelope / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Dolan KA / Brohawn SG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2022 Title: Structure of SARS-CoV-2 M protein in lipid nanodiscs. Authors: Kimberly A Dolan / Mandira Dutta / David M Kern / Abhay Kotecha / Gregory A Voth / Stephen G Brohawn / Abstract: SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other ...SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity in a simple lipid bilayer and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26993.map.gz | 85.8 MB | EMDB map data format | |
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Header (meta data) | emd-26993-v30.xml emd-26993.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_26993.png | 116.7 KB | ||
Filedesc metadata | emd-26993.cif.gz | 5.5 KB | ||
Others | emd_26993_half_map_1.map.gz emd_26993_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26993 | HTTPS FTP |
-Validation report
Summary document | emd_26993_validation.pdf.gz | 911.9 KB | Display | EMDB validaton report |
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Full document | emd_26993_full_validation.pdf.gz | 911.5 KB | Display | |
Data in XML | emd_26993_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_26993_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26993 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26993 | HTTPS FTP |
-Related structure data
Related structure data | 8ctkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11067 (Title: Structure of SARS-CoV-2 M protein in lipid nanodiscs / Data size: 4.0 TB Data #1: SARS-CoV-2 M protein in an MSP1E3D1 lipid nanodisc [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26993.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.727 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_26993_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26993_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : M protein
Entire | Name: M protein |
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Components |
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-Supramolecule #1: M protein
Supramolecule | Name: M protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 52 KDa |
-Macromolecule #1: Membrane protein
Macromolecule | Name: Membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 26.190693 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 1, wait time 5s, blot time 3s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 64966 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) |