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- PDB-8xz4: SARS-CoV-2 S and radixin complex structure -

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Basic information

Entry
Database: PDB / ID: 8xz4
TitleSARS-CoV-2 S and radixin complex structure
Components
  • Radixin
  • Spike protein S2'
KeywordsVIRAL PROTEIN/PROEIN BINDING / SARS-CoV-2 / S / ezrin-radixin-moesin / cytoskeleton / assembly / VIRAL/PROTEIN BINDING / VIRAL PROTEIN-PROEIN BINDING complex
Function / homology
Function and homology information


stereocilium base / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / positive regulation of early endosome to late endosome transport / microvillus assembly / negative regulation of adherens junction organization / regulation of Rap protein signal transduction / negative regulation of homotypic cell-cell adhesion ...stereocilium base / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / positive regulation of early endosome to late endosome transport / microvillus assembly / negative regulation of adherens junction organization / regulation of Rap protein signal transduction / negative regulation of homotypic cell-cell adhesion / negative regulation of GTPase activity / positive regulation of protein localization to early endosome / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / : / barbed-end actin filament capping / negative regulation of cell size / cellular response to thyroid hormone stimulus / establishment of endothelial barrier / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / regulation of GTPase activity / Sensory processing of sound by inner hair cells of the cochlea / protein kinase A binding / cortical actin cytoskeleton / regulation of cell size / microvillus / Recycling pathway of L1 / cleavage furrow / positive regulation of G1/S transition of mitotic cell cycle / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / ruffle / T-tubule / cell periphery / protein localization to plasma membrane / adherens junction / filopodium / apical part of cell / positive regulation of protein catabolic process / regulation of cell shape / lamellipodium / actin binding / ATPase binding / midbody / symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / positive regulation of cell migration / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular space / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane
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 / Radixin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.129 Å
AuthorsWang, J.M. / Ma, W.F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: SARS-CoV-2 S and radixin complex structure
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

Downloads & links

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Assembly

Deposited unit
A: Radixin
B: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)36,7702
Polymers36,7702
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.375, 77.375, 58.444
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 Radixin


Mass: 35181.609 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RDX / Production host: Escherichia coli (E. coli) / References: UniProt: P35241
#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.: 105 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 75 mM Sodium acetate, 0.1 M Tris-HCl, pH 7.4, 5.5% 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 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 19283 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.8 / Net I/σ(I): 21.1
Reflection shellResolution: 2.1→2.3 Å / Num. unique obs: 1389 / CC1/2: 0.96

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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: 2.129→38.688 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 1942 10.07 %
Rwork0.2161 --
obs0.221 19283 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.129→38.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 0 105 2634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042594
X-RAY DIFFRACTIONf_angle_d0.6473509
X-RAY DIFFRACTIONf_dihedral_angle_d5.4941561
X-RAY DIFFRACTIONf_chiral_restr0.044375
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1295-2.18270.29361370.27541254X-RAY DIFFRACTION100
2.1827-2.24170.26641410.25181233X-RAY DIFFRACTION100
2.2417-2.30770.27861370.2361249X-RAY DIFFRACTION100
2.3077-2.38210.29481380.26411228X-RAY DIFFRACTION100
2.3821-2.46730.35411380.24961261X-RAY DIFFRACTION100
2.4673-2.5660.26231370.25551219X-RAY DIFFRACTION100
2.566-2.68280.31451450.25871265X-RAY DIFFRACTION100
2.6828-2.82420.2961400.24641247X-RAY DIFFRACTION100
2.8242-3.00110.31661370.25191248X-RAY DIFFRACTION100
3.0011-3.23270.29791380.25061261X-RAY DIFFRACTION100
3.2327-3.55780.25591450.22211250X-RAY DIFFRACTION100
3.5578-4.07210.28451190.19451069X-RAY DIFFRACTION85
4.0721-5.12860.23321390.17941270X-RAY DIFFRACTION100
5.1286-38.6880.22421510.18891287X-RAY DIFFRACTION100

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