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- PDB-8i5h: Crystal structure of SARS-CoV-2 delta variant spike receptor-bind... -

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Basic information

Entry
Database: PDB / ID: 8i5h
TitleCrystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 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 / VIRUS
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: 2.38 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 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
D: Spike protein S1
E: Fab Heavy chain
F: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,86312
Polymers209,1999
Non-polymers6643
Water5,332296
1
R: Spike protein S1
H: Fab Heavy chain
L: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9544
Polymers69,7333
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-23 kcal/mol
Surface area27110 Å2
MethodPISA
2
A: Spike protein S1
B: Fab Heavy chain
C: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9544
Polymers69,7333
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-24 kcal/mol
Surface area26910 Å2
MethodPISA
3
D: Spike protein S1
E: Fab Heavy chain
F: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9544
Polymers69,7333
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-22 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.805, 113.730, 272.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 21844.504 Da / Num. of mol.: 3 / Fragment: Delta RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Variant: delta / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody Fab Heavy chain


Mass: 24611.613 Da / Num. of mol.: 3
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: 23276.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: pH 6.5 100 mM Bis-Tris, 17.5% PEG 10K, 100 mM Ammonium acetate, 5% Glycerol

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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: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.38→99.9 Å / Num. obs: 111340 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 78649 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→42.977 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 5532 4.98 %
Rwork0.1883 --
obs0.1904 111174 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→42.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14277 0 42 296 14615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814709
X-RAY DIFFRACTIONf_angle_d0.98220031
X-RAY DIFFRACTIONf_dihedral_angle_d11.4328750
X-RAY DIFFRACTIONf_chiral_restr0.0542221
X-RAY DIFFRACTIONf_plane_restr0.0072583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4070.34831600.28563544X-RAY DIFFRACTION100
2.407-2.43540.32441990.28523412X-RAY DIFFRACTION100
2.4354-2.46510.33891740.27923516X-RAY DIFFRACTION100
2.4651-2.49630.33681700.27113451X-RAY DIFFRACTION100
2.4963-2.52910.38041840.27013495X-RAY DIFFRACTION100
2.5291-2.56370.34141730.26383469X-RAY DIFFRACTION100
2.5637-2.60040.35092000.24753470X-RAY DIFFRACTION100
2.6004-2.63920.33161470.24963505X-RAY DIFFRACTION100
2.6392-2.68040.26191900.23523507X-RAY DIFFRACTION100
2.6804-2.72430.31811850.22913479X-RAY DIFFRACTION100
2.7243-2.77130.24941760.22433534X-RAY DIFFRACTION100
2.7713-2.82170.28161720.22243453X-RAY DIFFRACTION100
2.8217-2.8760.3011440.22943542X-RAY DIFFRACTION100
2.876-2.93460.29721720.23693516X-RAY DIFFRACTION100
2.9346-2.99840.2991970.23943472X-RAY DIFFRACTION100
2.9984-3.06820.27531870.22773515X-RAY DIFFRACTION100
3.0682-3.14490.27042240.22923453X-RAY DIFFRACTION100
3.1449-3.22990.28911780.23053490X-RAY DIFFRACTION100
3.2299-3.32490.26441960.21843508X-RAY DIFFRACTION100
3.3249-3.43220.24261970.20733517X-RAY DIFFRACTION100
3.4322-3.55480.24172070.19593506X-RAY DIFFRACTION100
3.5548-3.6970.24771810.19843540X-RAY DIFFRACTION100
3.697-3.86520.22891720.18113533X-RAY DIFFRACTION100
3.8652-4.06880.2081990.16743521X-RAY DIFFRACTION100
4.0688-4.32350.18331830.15273541X-RAY DIFFRACTION100
4.3235-4.6570.1481920.13593563X-RAY DIFFRACTION100
4.657-5.12490.19811920.14243553X-RAY DIFFRACTION100
5.1249-5.86490.21072030.1613585X-RAY DIFFRACTION100
5.8649-7.38310.19181830.17053659X-RAY DIFFRACTION100
7.3831-42.9770.17261950.15393793X-RAY DIFFRACTION100

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