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Yorodumi- PDB-9ctw: Cryo-EM structure of SARS-CoV-2 M (long conformation) in the pres... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ctw | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / SARS-COV-2 / CORONAVIRUS / VIRAL PROTEIN / CAPSID PROTEIN | ||||||
Function / homology | Function and homology information Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / 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 / endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi membrane / CD28 dependent PI3K/Akt signaling / 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 | Mus musculus (house mouse) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å | ||||||
Authors | Dolan, K.A. / Brohawn, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly Authors: Dutta, M. / Dolan, K.A. / Amiar, S. / Bass, E.J. / Sultana, R. / Voth, G.A. / Brohawn, S.G. / Stahelin, R.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ctw.cif.gz | 251 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ctw.ent.gz | 200 KB | Display | PDB format |
PDBx/mmJSON format | 9ctw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ctw_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9ctw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9ctw_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 9ctw_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/9ctw ftp://data.pdbj.org/pub/pdb/validation_reports/ct/9ctw | HTTPS FTP |
-Related structure data
Related structure data | 45921MC 9ctuC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 26247.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) #2: Antibody | Mass: 28394.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) #3: Protein | Mass: 26190.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC5 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: M protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.052 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190251 / Symmetry type: POINT | ||||||||||||||||||||||||
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