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- PDB-8xz6: MERS-CoV S and radixin complex structure -

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Basic information

Entry
Database: PDB / ID: 8xz6
TitleMERS-CoV S and radixin complex structure
Components
  • Radixin
  • Spike protein S2'
KeywordsVIRAL PROTEIN/PROTEIN BINDING / MERS-CoV / S / ezrin-radixin-moesin / cytoskeleton / assembly / VIRAL PROTEIN-PROTEIN 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 / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / positive regulation of cell migration / apical plasma membrane / cadherin binding / 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 / host cell plasma membrane / virion membrane / extracellular space / RNA binding / extracellular exosome / 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 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / 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 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / 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 / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / 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)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsWang, J.M. / Ma, W.F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: MERS-CoV 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: Radixin
C: Radixin
D: Radixin
E: Spike protein S2'
F: Spike protein S2'
G: Spike protein S2'
H: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)148,1428
Polymers148,1428
Non-polymers00
Water9,098505
1
A: Radixin
H: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)37,0362
Polymers37,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-3 kcal/mol
Surface area16690 Å2
MethodPISA
2
B: Radixin
G: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)37,0362
Polymers37,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area16520 Å2
MethodPISA
3
C: Radixin
E: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)37,0362
Polymers37,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-5 kcal/mol
Surface area16990 Å2
MethodPISA
4
D: Radixin
F: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)37,0362
Polymers37,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-4 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.310, 94.100, 134.300
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Radixin


Mass: 35325.738 Da / Num. of mol.: 4
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: 1709.814 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus
References: UniProt: K9N5Q8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, and 6% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 98890 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 12.5
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 7294 / CC1/2: 0.725

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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: 2.12→32.885 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 4933 4.99 %
Rwork0.2201 --
obs0.222 98889 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→32.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10107 0 0 505 10612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510426
X-RAY DIFFRACTIONf_angle_d0.76914077
X-RAY DIFFRACTIONf_dihedral_angle_d5.9636301
X-RAY DIFFRACTIONf_chiral_restr0.0461486
X-RAY DIFFRACTIONf_plane_restr0.0051813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.14410.40181400.33773141X-RAY DIFFRACTION99
2.1441-2.16930.36641610.33073092X-RAY DIFFRACTION100
2.1693-2.19580.32091530.32763156X-RAY DIFFRACTION99
2.1958-2.22350.33661550.32413118X-RAY DIFFRACTION100
2.2235-2.25280.35981650.29793106X-RAY DIFFRACTION100
2.2528-2.28370.36161420.29033155X-RAY DIFFRACTION100
2.2837-2.31630.29671590.28233100X-RAY DIFFRACTION100
2.3163-2.35080.32861530.27443197X-RAY DIFFRACTION100
2.3508-2.38760.3431600.28083066X-RAY DIFFRACTION100
2.3876-2.42670.32441640.25923127X-RAY DIFFRACTION100
2.4267-2.46850.32871840.25173064X-RAY DIFFRACTION100
2.4685-2.51340.30151950.25683144X-RAY DIFFRACTION100
2.5134-2.56170.29171640.25843098X-RAY DIFFRACTION100
2.5617-2.6140.32651640.23963142X-RAY DIFFRACTION100
2.614-2.67080.25711730.23713097X-RAY DIFFRACTION100
2.6708-2.73290.28651790.22963120X-RAY DIFFRACTION100
2.7329-2.80120.31451800.23593110X-RAY DIFFRACTION100
2.8012-2.87690.26291550.23333122X-RAY DIFFRACTION100
2.8769-2.96150.25821650.2333129X-RAY DIFFRACTION100
2.9615-3.0570.32251660.23863152X-RAY DIFFRACTION100
3.057-3.16620.27421400.25183148X-RAY DIFFRACTION100
3.1662-3.29290.2781370.22823158X-RAY DIFFRACTION100
3.2929-3.44260.25711740.22763128X-RAY DIFFRACTION100
3.4426-3.62390.24741560.21523154X-RAY DIFFRACTION100
3.6239-3.85060.24081900.19713115X-RAY DIFFRACTION100
3.8506-4.14740.20991810.18473126X-RAY DIFFRACTION100
4.1474-4.56370.241690.17893147X-RAY DIFFRACTION100
4.5637-5.22190.19921810.183144X-RAY DIFFRACTION100
5.2219-6.57040.23261540.20943190X-RAY DIFFRACTION100
6.5704-32.880.1991740.18373210X-RAY DIFFRACTION99

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