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- PDB-8ydp: Crystal structure of the receptor binding domain of SARS-CoV-2 sp... -

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Basic information

Entry
Database: PDB / ID: 8ydp
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9
Components
  • SARS-CoV-2 inhibiting peptide Ce9
  • 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 / Virion Assembly and Release / host cell surface / 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 / Virion Assembly and Release / host cell surface / 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 / 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 / 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: 2.3 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 Ce9
B: Spike protein S1
C: SARS-CoV-2 inhibiting peptide Ce9
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,95011
Polymers62,0474
Non-polymers9037
Water2,828157
1
A: SARS-CoV-2 inhibiting peptide Ce9
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5216
Polymers31,0242
Non-polymers4974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-4 kcal/mol
Surface area12130 Å2
MethodPISA
2
C: SARS-CoV-2 inhibiting peptide Ce9
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4295
Polymers31,0242
Non-polymers4053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-3 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.295, 72.295, 100.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein/peptide SARS-CoV-2 inhibiting peptide Ce9


Mass: 4825.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Spike protein S1


Mass: 26198.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.22 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.5), 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26011 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rsym value: 0.151 / Net I/σ(I): 13.81
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 4174 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.12 Å / SU ML: 0.3926 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.4271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 1334 5.14 %
Rwork0.2122 24627 -
obs0.2148 25961 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 58 157 4018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183952
X-RAY DIFFRACTIONf_angle_d0.41775347
X-RAY DIFFRACTIONf_chiral_restr0.0404560
X-RAY DIFFRACTIONf_plane_restr0.0032695
X-RAY DIFFRACTIONf_dihedral_angle_d11.06691432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.36421460.34062437X-RAY DIFFRACTION99.23
2.38-2.480.36461430.32152457X-RAY DIFFRACTION99.88
2.48-2.590.32471230.28452492X-RAY DIFFRACTION99.92
2.59-2.730.33571380.26552438X-RAY DIFFRACTION99.84
2.73-2.90.34961300.24142469X-RAY DIFFRACTION99.85
2.9-3.120.28811190.25652479X-RAY DIFFRACTION99.73
3.12-3.440.28651350.22642475X-RAY DIFFRACTION100
3.44-3.930.2511300.18692438X-RAY DIFFRACTION99.96
3.93-4.950.20471370.16972471X-RAY DIFFRACTION99.96
4.96-39.120.22681330.18312471X-RAY DIFFRACTION99.92

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