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- EMDB-23665: Structural basis for SARS-CoV-2 envelope protein in recognition o... -

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Basic information

Entry
Database: EMDB / ID: EMD-23665
TitleStructural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1
Map dataCryosparc non-uniform refinement without sharpening
Sample
  • Complex: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains
    • Protein or peptide: MAGUK p55 subfamily member 5
    • Protein or peptide: Envelope small membrane protein
KeywordsSARS-CoV-2 envelope protein / PDZ-binding motif / complex / pathogen-host interaction / CELL ADHESION-VIRAL PROTEIN complex
Function / homology
Function and homology information


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 / myelin sheath adaxonal region ...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 / myelin sheath adaxonal region / lateral loop / regulation of transforming growth factor beta receptor signaling pathway / Regulation of gap junction activity / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / apical junction complex / generation of neurons / central nervous system neuron development / host cell Golgi membrane / bicellular tight junction / endoplasmic reticulum-Golgi intermediate compartment / Maturation of protein E / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / : / gene expression / monoatomic ion channel activity / perikaryon / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / apical plasma membrane / axon / protein domain specific binding / 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
L27-N / MPP5, SH3 domain / L27_N / Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / L27 domain, C-terminal / L27 domain ...L27-N / MPP5, SH3 domain / L27_N / Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Envelope small membrane protein / Protein PALS1
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsLiu Q / Chai J
CitationJournal: 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
DepositionMar 22, 2021-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m4r
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23665.png

Downloads & links

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Map

FileDownload / File: emd_23665.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc non-uniform refinement without sharpening
Voxel sizeX=Y=Z: 0.684 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.35293797 - 0.9423707
Average (Standard dev.)0.002212569 (±0.03260368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 175.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6840.6840.684
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z175.104175.104175.104
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3530.9420.002

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Supplemental data

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Sample components

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Entire : Complex structure of SARS-CoV-2 envelope protein Ec18 and human P...

EntireName: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains
Components
  • Complex: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains
    • Protein or peptide: MAGUK p55 subfamily member 5
    • Protein or peptide: Envelope small membrane protein

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Supramolecule #1: Complex structure of SARS-CoV-2 envelope protein Ec18 and human P...

SupramoleculeName: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: MAGUK p55 subfamily member 5

MacromoleculeName: MAGUK p55 subfamily member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.780504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAPITDERV YESIGQYGGE TVKIVRIEKA RDIPLGATVR NEMDSVIISR IVKGGAAEKS GLLHEGDEVL EINGIEIRGK DVNEVFDLL SDMHGTLTFV LIPSQQIKPP PAKETVIHVK AHFDYDPSDD PYVPCRELGL SFQKGDILHV ISQEDPNWWQ A YREGDEDN ...String:
SNAPITDERV YESIGQYGGE TVKIVRIEKA RDIPLGATVR NEMDSVIISR IVKGGAAEKS GLLHEGDEVL EINGIEIRGK DVNEVFDLL SDMHGTLTFV LIPSQQIKPP PAKETVIHVK AHFDYDPSDD PYVPCRELGL SFQKGDILHV ISQEDPNWWQ A YREGDEDN QPLAGLVPGK EEILTYEEMS LYHQPANRKR PIILIGPQNC GQNELRQRLM NKEKDRFASA VPHTTRSRRD QE VAGRDYH FVSRQAFEAD IAAGKFIEHG EFEKNLYGTS IDSVRQVINS GKICLLSLRT QSLKTLRNSD LKPYIIFIAP PSQ ERLRAL LAKEGKNPKP EELREIIEKT REMEQNNGHY FDTAIVNSDL DKAYQELLRL INKLDTEPQW VPSTWLR

UniProtKB: Protein PALS1, Protein PALS1

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Macromolecule #2: Envelope small membrane protein

MacromoleculeName: Envelope small membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 2.062395 KDa
SequenceString:
VYSRVKNLNS SRVPDLLV

UniProtKB: Envelope small membrane protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47615
FSC plot (resolution estimation)

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