[English] 日本語
Yorodumi
- EMDB-23665: Structural basis for SARS-CoV-2 envelope protein in recognition o... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_23665.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 256 pix.
= 175.104 Å		0.68 Å/pix.
x 256 pix.
= 175.104 Å		0.68 Å/pix.
x 256 pix.
= 175.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.684 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more