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- PDB-8ydu: Crystal structure of the receptor binding domain of SARS-CoV-2 Om... -

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Basic information

Entry
Database: PDB / ID: 8ydu
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE
Components
  • SARS-CoV-2 inhibiting peptide CeSPIACE
  • Spike protein S1
KeywordsVIRAL PROTEIN/INHIBITOR / RBD / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / host extracellular space / 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 ...Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / host extracellular space / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / 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 / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNakamura, S. / Numoto, N. / Fujiyoshi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0108462, JP21fk0108585, JP21ae0121028, JP18ae0101046 Japan
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
CitationJournal: To Be Published
Title: Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
Authors: Nakamura, S. / Tanimura, Y. / Nomura, R. / Suzuki, H. / Nishikawa, K. / Kamegawa, A. / Numoto, N. / Tanaka, A. / Kawabata, S. / Sakaguchi, S. / Emi, A. / Suzuki, Y. / Fujiyoshi, Y.
History
DepositionFeb 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SARS-CoV-2 inhibiting peptide CeSPIACE
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1183
Polymers31,0262
Non-polymers921
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-6 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.260, 74.260, 99.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

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Components

#1: Protein/peptide SARS-CoV-2 inhibiting peptide CeSPIACE


Mass: 4721.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Spike protein S1


Mass: 26304.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-Tris (pH 5.5), 0.1 M ammonium acetate, 17% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 40065 / % possible obs: 99.3 % / Redundancy: 8.3 % / Biso Wilson estimate: 32.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.44
Reflection shellResolution: 1.63→1.73 Å / Num. unique obs: 6419 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.41 Å / SU ML: 0.2395 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2523 1772 5.01 %
Rwork0.2201 33586 -
obs0.2218 35358 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 6 154 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581918
X-RAY DIFFRACTIONf_angle_d0.70962599
X-RAY DIFFRACTIONf_chiral_restr0.049274
X-RAY DIFFRACTIONf_plane_restr0.0063337
X-RAY DIFFRACTIONf_dihedral_angle_d12.5606686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.43491310.40882531X-RAY DIFFRACTION98.08
1.75-1.80.43511340.372514X-RAY DIFFRACTION98.62
1.8-1.860.35281370.32462575X-RAY DIFFRACTION98.91
1.86-1.920.32311280.30852512X-RAY DIFFRACTION98.91
1.92-20.35621340.29032552X-RAY DIFFRACTION98.9
2-2.090.33361350.26662564X-RAY DIFFRACTION99.41
2.09-2.20.31831350.26982548X-RAY DIFFRACTION99.26
2.2-2.340.30351370.25282584X-RAY DIFFRACTION99.45
2.34-2.520.28321350.24322568X-RAY DIFFRACTION99.7
2.52-2.770.31251360.24122612X-RAY DIFFRACTION99.85
2.77-3.170.25151370.21872617X-RAY DIFFRACTION99.93
3.17-40.22791440.19692645X-RAY DIFFRACTION100
4-39.410.1831490.17342764X-RAY DIFFRACTION99.83

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