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Yorodumi- PDB-7m4r: Structural basis for SARS-CoV-2 envelope protein in recognition o... -
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-Basic information
Entry | Database: PDB / ID: 7m4r | ||||||
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Title | Structural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1 | ||||||
Components |
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Keywords | CELL ADHESION/VIRAL PROTEIN / SARS-CoV-2 envelope protein / PDZ-binding motif / complex / pathogen-host interaction / CELL ADHESION-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information disruption of cellular anatomical structure in another organism / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly ...disruption of cellular anatomical structure in another organism / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / viral budding from Golgi membrane / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Regulation of gap junction activity / Schmidt-Lanterman incisure / peripheral nervous system myelin maintenance / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / generation of neurons / central nervous system neuron development / host cell Golgi membrane / endoplasmic reticulum-Golgi intermediate compartment / bicellular tight junction / Maturation of protein E / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / monoatomic ion channel activity / gene expression / perikaryon / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / apical plasma membrane / protein domain specific binding / axon / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||
Authors | Liu, Q. / Chai, J. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1. Authors: Jin Chai / Yuanheng Cai / Changxu Pang / Liguo Wang / Sean McSweeney / John Shanklin / Qun Liu / Abstract: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has created global health and economic emergencies. SARS-CoV-2 viruses promote their own spread and virulence by hijacking human proteins, which ...The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has created global health and economic emergencies. SARS-CoV-2 viruses promote their own spread and virulence by hijacking human proteins, which occurs through viral protein recognition of human targets. To understand the structural basis for SARS-CoV-2 viral-host protein recognition, here we use cryo-electron microscopy (cryo-EM) to determine a complex structure of the human cell junction protein PALS1 and SARS-CoV-2 viral envelope (E) protein. Our reported structure shows that the E protein C-terminal DLLV motif recognizes a pocket formed exclusively by hydrophobic residues from the PDZ and SH3 domains of PALS1. Our structural analysis provides an explanation for the observation that the viral E protein recruits PALS1 from lung epithelial cell junctions. In addition, our structure provides novel targets for peptide- and small-molecule inhibitors that could block the PALS1-E interactions to reduce E-mediated virulence. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7m4r.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m4r.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 7m4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m4r_validation.pdf.gz | 811.2 KB | Display | wwPDB validaton report |
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Full document | 7m4r_full_validation.pdf.gz | 817.5 KB | Display | |
Data in XML | 7m4r_validation.xml.gz | 28 KB | Display | |
Data in CIF | 7m4r_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/7m4r ftp://data.pdbj.org/pub/pdb/validation_reports/m4/7m4r | HTTPS FTP |
-Related structure data
Related structure data | 23665MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 44780.504 Da / Num. of mol.: 2 / Fragment: UNP residues 236-410,461-675 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPP5, PALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3R9 #2: Protein/peptide | | Mass: 2062.395 Da / Num. of mol.: 1 / Fragment: UNP residues 58-75 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC4 |
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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: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
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 |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47615 / Symmetry type: POINT | ||||||||||||||||||||||||
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