[English] 日本語
![](img/lk-miru.gif)
- PDB-7vgs: SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vgs | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / M protein / viral structural protein / virus assembly / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Zhang, Z. / Ohto, U. / Shimizu, T. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 268.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 210 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 843.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 857.5 KB | Display | |
Data in XML | ![]() | 38.4 KB | Display | |
Data in CIF | ![]() | 58.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31978MC ![]() 7vgrC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data #2: M protein (LMNG/CHS) + Fab-E [micrographs - multiframe] Data #3: M protein (LMNG/CHS) + Fab-B [micrographs - multiframe]) |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 28257.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() #2: Antibody | Mass: 23999.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Antibody | Mass: 24499.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 61.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22011 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
|