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Yorodumi- EMDB-31978: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31978 | |||||||||
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Title | SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / cytoplasmic capsid assembly / CD28 dependent PI3K/Akt signaling / host cell Golgi membrane / 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 / CD28 dependent PI3K/Akt signaling / host cell Golgi membrane / 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 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Zhang Z / Ohto U / Shimizu T | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31978.map.gz | 27.6 MB | EMDB map data format | |
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Header (meta data) | emd-31978-v30.xml emd-31978.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_31978.png | 65.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31978 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31978 | HTTPS FTP |
-Validation report
Summary document | emd_31978_validation.pdf.gz | 497.6 KB | Display | EMDB validaton report |
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Full document | emd_31978_full_validation.pdf.gz | 497.1 KB | Display | |
Data in XML | emd_31978_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_31978_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31978 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31978 | HTTPS FTP |
-Related structure data
Related structure data | 7vgsMC 7vgrC 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-11168 (Title: Structure of SARS-CoV-2 membrane protein / Data size: 4.4 TB / Data #1: M protein (LMNG/CHS) [micrographs - multiframe] Data #2: M protein (LMNG/CHS) + Fab-E [micrographs - multiframe] Data #3: M protein (LMNG/CHS) + Fab-B [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_31978.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Entire | Name: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Supramolecule | Name: 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
Supramolecule | Name: Membrane protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: YN7717_9 Fab
Supramolecule | Name: YN7717_9 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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: 28.257822 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: YN7717_9 Fab light chain
Macromolecule | Name: YN7717_9 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.999266 KDa |
Sequence | String: 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 |
-Macromolecule #3: YN7717_9 Fab heavy chain
Macromolecule | Name: YN7717_9 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 24.499639 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.6 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22011 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7vgs: |