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- PDB-7m4r: Structural basis for SARS-CoV-2 envelope protein in recognition o... -

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Basic information

Entry
Database: PDB / ID: 7m4r
TitleStructural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1
Components
  • Envelope small membrane protein
  • MAGUK p55 subfamily member 5
KeywordsCELL 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


protein localization to myelin sheath abaxonal region / disruption of cellular anatomical structure in another organism / SARS-CoV-1 targets PDZ proteins in cell-cell junction / symbiont-mediated perturbation of host cell endomembrane system / viral budding from Golgi membrane / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction ...protein localization to myelin sheath abaxonal region / disruption of cellular anatomical structure in another organism / SARS-CoV-1 targets PDZ proteins in cell-cell junction / symbiont-mediated perturbation of host cell endomembrane system / viral budding from Golgi membrane / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Regulation of gap junction activity / lateral loop / 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 / Maturation of protein E / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / perikaryon / Translation of Structural Proteins / Virion Assembly and Release / gene expression / Induction of Cell-Cell Fusion / 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 / identical protein binding / membrane / 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
MethodELECTRON MICROSCOPY / single 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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 31, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: MAGUK p55 subfamily member 5
B: MAGUK p55 subfamily member 5
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)91,6233
Polymers91,6233
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MAGUK p55 subfamily member 5 / cell junction protein PALS1


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 Envelope small membrane protein / E / sM protein


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex structure of SARS-CoV-2 envelope protein Ec18 and human PALS1 PSG domains
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47615 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0075194
ELECTRON MICROSCOPYf_angle_d0.7747034
ELECTRON MICROSCOPYf_dihedral_angle_d13.882701
ELECTRON MICROSCOPYf_chiral_restr0.049774
ELECTRON MICROSCOPYf_plane_restr0.005927

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