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- PDB-7wn2: Crystal structure of SARS-CoV-2 spike receptor-binding domain (RB... -

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Basic information

Entry
Database: PDB / ID: 7wn2
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab
Components
  • Fab Heavy chain
  • Fab Light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / spike / coronavirus / viral protein / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / 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 / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / 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 / 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, 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 ...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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYamamoto, A. / Higashiura, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / ...Authors: Shitaoka, K. / Higashiura, A. / Kawano, Y. / Yamamoto, A. / Mizoguchi, Y. / Hashiguchi, T. / Nishimichi, N. / Huang, S. / Ito, A. / Ohki, S. / Kanda, M. / Taniguchi, T. / Yoshizato, R. / Azuma, H. / Kitajima, Y. / Yokosaki, Y. / Okada, S. / Sakaguchi, T. / Yasuda, T.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Spike protein S1
H: Fab Heavy chain
L: Fab Light chain
A: Spike protein S1
B: Fab Heavy chain
C: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,35815
Polymers145,2436
Non-polymers1,1159
Water4,396244
1
R: Spike protein S1
H: Fab Heavy chain
L: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1317
Polymers72,6213
Non-polymers5094
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-65 kcal/mol
Surface area28140 Å2
MethodPISA
2
A: Spike protein S1
B: Fab Heavy chain
C: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2278
Polymers72,6213
Non-polymers6055
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-67 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.265, 118.195, 196.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules HBLC

#2: Antibody Fab Heavy chain


Mass: 24241.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab Light chain


Mass: 23119.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 4 molecules RA

#1: Protein Spike protein S1


Mass: 25260.320 Da / Num. of mol.: 2 / Fragment: Receptor-binding domain
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
#5: 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: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 251 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.25 M ammonium sulfate, 22.5% PEG3350, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.35→46.71 Å / Num. obs: 74372 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.982 / Net I/σ(I): 4.1
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4462 / CC1/2: 0.685 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EAM, 7CHB, 6XDG

7eam

7chb

6xdg


Resolution: 2.35→46.71 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 3688 4.98 %
Rwork0.2282 --
obs0.2307 74092 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9661 0 63 244 9968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089974
X-RAY DIFFRACTIONf_angle_d1.02513568
X-RAY DIFFRACTIONf_dihedral_angle_d16.7253568
X-RAY DIFFRACTIONf_chiral_restr0.0611505
X-RAY DIFFRACTIONf_plane_restr0.0081737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.48691400.43632636X-RAY DIFFRACTION97
2.38-2.410.41161310.38672686X-RAY DIFFRACTION99
2.41-2.450.40851610.37872621X-RAY DIFFRACTION100
2.45-2.480.45241350.36232724X-RAY DIFFRACTION100
2.48-2.520.39611630.33512638X-RAY DIFFRACTION99
2.52-2.560.41041450.31742675X-RAY DIFFRACTION99
2.56-2.610.33291350.3062696X-RAY DIFFRACTION99
2.61-2.660.35131470.30122670X-RAY DIFFRACTION99
2.66-2.710.36411460.29512671X-RAY DIFFRACTION99
2.71-2.760.34281420.29822699X-RAY DIFFRACTION100
2.76-2.820.35351330.29252700X-RAY DIFFRACTION99
2.82-2.890.34991410.28592684X-RAY DIFFRACTION99
2.89-2.960.32191230.28672726X-RAY DIFFRACTION99
2.96-3.040.33321540.28122661X-RAY DIFFRACTION99
3.04-3.130.37951540.26322689X-RAY DIFFRACTION100
3.13-3.230.29241490.25622688X-RAY DIFFRACTION99
3.23-3.350.33221340.24142729X-RAY DIFFRACTION100
3.35-3.480.30741470.24572714X-RAY DIFFRACTION99
3.48-3.640.30431360.2262723X-RAY DIFFRACTION99
3.64-3.830.27481380.2172708X-RAY DIFFRACTION99
3.83-4.070.22771510.18642703X-RAY DIFFRACTION99
4.07-4.380.1751520.15982739X-RAY DIFFRACTION99
4.38-4.830.1511310.13412737X-RAY DIFFRACTION99
4.83-5.520.20831280.15142780X-RAY DIFFRACTION99
5.52-6.950.22021270.19172833X-RAY DIFFRACTION100
6.95-46.710.22891450.20242874X-RAY DIFFRACTION97

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