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- PDB-8xz0: Crystal complex structure of SARS-CoV-2 S bound to human ezrin -

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Basic information

Entry
Database: PDB / ID: 8xz0
TitleCrystal complex structure of SARS-CoV-2 S bound to human ezrin
Components
  • Ezrin
  • Spike protein S2'
KeywordsVIRAL PROTEIN/PROTEIN BINDING / SARS-CoV-2 / spike / ezrin-radixin-moesin / ERM / COVID-19 / cytoskeleton / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / regulation of microvillus length / regulation of organelle assembly / establishment or maintenance of apical/basal cell polarity / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / microvillus assembly / membrane to membrane docking ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / regulation of microvillus length / regulation of organelle assembly / establishment or maintenance of apical/basal cell polarity / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / microvillus assembly / membrane to membrane docking / Netrin-1 signaling / establishment of centrosome localization / uropod / astral microtubule organization / negative regulation of p38MAPK cascade / positive regulation of protein localization to early endosome / : / cortical microtubule organization / filopodium assembly / protein-containing complex localization / positive regulation of multicellular organism growth / sphingosine-1-phosphate receptor signaling pathway / S100 protein binding / establishment of endothelial barrier / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of interleukin-2 production / leukocyte cell-cell adhesion / negative regulation of T cell receptor signaling pathway / protein kinase A binding / microvillus membrane / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / cortical cytoskeleton / microvillus / Recycling pathway of L1 / brush border / actin filament bundle assembly / immunological synapse / plasma membrane raft / cell adhesion molecule binding / ruffle / cellular response to cAMP / cell periphery / protein localization to plasma membrane / cell projection / positive regulation of protein localization to plasma membrane / adherens junction / actin filament / filopodium / negative regulation of ERK1 and ERK2 cascade / receptor internalization / ruffle membrane / fibrillar center / apical part of cell / positive regulation of protein catabolic process / disordered domain specific binding / actin filament binding / regulation of cell shape / actin cytoskeleton / actin binding / ATPase binding / actin cytoskeleton organization / symbiont-mediated disruption of host tissue / basolateral plasma membrane / microtubule binding / Maturation of spike protein / vesicle / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endosome / host cell surface receptor binding / ciliary basal body / symbiont-mediated suppression of host innate immune response / apical plasma membrane / cadherin binding / receptor ligand activity / endocytosis involved in viral entry into host cell / protein domain specific binding / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of gene expression / symbiont entry into host cell / virion attachment to host cell / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Spike glycoprotein / Ezrin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.035 Å
AuthorsWang, J.M. / Ma, W.F.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentNone China
CitationJournal: To Be Published
Title: Crystal complex structure of SARS-CoV-2 S bound to human ezrin
Authors: Wang, J.M. / Ma, W.F.
History
DepositionJan 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ezrin
B: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)36,5712
Polymers36,5712
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.507, 77.507, 55.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Ezrin / Cytovillin / Villin-2 / p81


Mass: 34982.477 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZR, VIL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P15311
#2: Protein/peptide Spike protein S2'


Mass: 1588.822 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.22 M Magnesium acetate and 19% PEG 3350,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18767 / % possible obs: 100 % / Redundancy: 16.7 % / CC1/2: 0.85 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 2092 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.035→34.662 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1006 5.36 %
Rwork0.2148 --
obs0.217 18767 87.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.035→34.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 0 89 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082485
X-RAY DIFFRACTIONf_angle_d0.9363365
X-RAY DIFFRACTIONf_dihedral_angle_d7.5341482
X-RAY DIFFRACTIONf_chiral_restr0.053365
X-RAY DIFFRACTIONf_plane_restr0.006429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0353-2.14250.3334400.2822773X-RAY DIFFRACTION27
2.1425-2.27680.30051010.27762515X-RAY DIFFRACTION85
2.2768-2.45250.28911810.25822851X-RAY DIFFRACTION100
2.4525-2.69920.29841870.25152848X-RAY DIFFRACTION100
2.6992-3.08960.2681630.23712913X-RAY DIFFRACTION100
3.0896-3.89170.27611490.20342905X-RAY DIFFRACTION99
3.8917-34.6620.21431850.18842956X-RAY DIFFRACTION100

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