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- PDB-7qcs: PALS1/MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide -

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Basic information

Entry
Database: PDB / ID: 7qcs
TitlePALS1/MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide
Components
  • Envelope small membrane protein
  • Protein PALS1
KeywordsCELL ADHESION / PALS1-MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide
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 / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsZhu, Y. / Alvarez, F. / Haouz, A. / Mechaly, A. / Caillet-Saguy, C.
Funding support France, 3items
OrganizationGrant numberCountry
Pasteur InstituteURGENCE COVID-19 fundraising campaign France
Agence Nationale de la Recherche (ANR)Recherche Action Covid19 FRM PDZCov2 program France
Pasteur InstituteDON MICHELIN COVID PFR-5 Cov-2-Cvnet France
CitationJournal: Front Microbiol / Year: 2022
Title: Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.
Authors: Zhu, Y. / Alvarez, F. / Wolff, N. / Mechaly, A. / Brule, S. / Neitthoffer, B. / Etienne-Manneville, S. / Haouz, A. / Boeda, B. / Caillet-Saguy, C.
History
DepositionNov 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PALS1
B: Protein PALS1
C: Envelope small membrane protein
D: Envelope small membrane protein
E: Protein PALS1


Theoretical massNumber of molelcules
Total (without water)35,4255
Polymers35,4255
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.75, 131.55, 70.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein PALS1 / MAGUK p55 subfamily member 5 / Membrane protein / palmitoylated 5 / Protein associated with Lin-7 1


Mass: 10923.343 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALS1, MPP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3R9
#2: Protein/peptide Envelope small membrane protein / E / sM protein


Mass: 1327.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: E, 4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.5 M LiCl, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.804→44.38 Å / Num. obs: 8040 / % possible obs: 75.85 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1238 / Net I/σ(I): 9.33
Reflection shellResolution: 2.804→2.904 Å / Num. unique obs: 799 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uu5

4uu5


Resolution: 2.804→44.38 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.479
RfactorNum. reflection% reflectionSelection details
Rfree0.3049 402 -RANDOM
Rwork0.2633 ---
obs0.2653 8039 76.5 %-
Displacement parametersBiso mean: 89.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.6045 Å20 Å20 Å2
2--12.682 Å20 Å2
3----11.0775 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.804→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 0 2204
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092223HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.132995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d815SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes383HARMONIC5
X-RAY DIFFRACTIONt_it2223HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1470SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.97
LS refinement shellResolution: 2.804→2.85 Å
RfactorNum. reflection% reflection
Rfree0.3773 20 -
Rwork0.3126 --
obs--77.41 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43191.2421-0.89873.3075-1.95440.8529-0.1328-0.0285-0.0425-0.02850.0012-0.0235-0.0425-0.02350.1316-0.075-0.0171-0.0434-0.0845-0.04210.080510.01536.840713.468
22.46681.43390.3695.25921.55280.6401-0.2099-0.08430.0319-0.08430.119-0.01330.0319-0.01330.0909-0.1141-0.01780.0171-0.09240.02990.029134.528236.705713.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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