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- PDB-8k3k: The crystal structure of nanobody Nb4 in complex with receptor bi... -

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Basic information

Entry
Database: PDB / ID: 8k3k
TitleThe crystal structure of nanobody Nb4 in complex with receptor binding domain (RBD) of BA.1 Spike protein
Components
  • Nanobody Nb4
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Nanobody / Receptor binding domain / SARS-CoV-2 / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 / suppression by virus 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / 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 / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsWang, H.Y. / Xu, W.Q.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentstart-up fund from the ShanghaiTech University China
CitationJournal: MedComm (2020) / Year: 2023
Title: A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
Authors: Hebang Yao / Hongyang Wang / Zhaoyong Zhang / Yuchi Lu / Zhiying Zhang / Yu Zhang / Xinyi Xiong / Yanqun Wang / Zhizhi Wang / Haitao Yang / Jincun Zhao / Wenqing Xu /
Abstract: SARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the ...SARS-CoV-2 viruses are highly transmissible and immune evasive. It is critical to develop broad-spectrum prophylactic and therapeutic antibodies for potential future pandemics. Here, we used the phage display method to discover nanobodies (Nbs) for neutralizing SARS-CoV-2 viruses especially Omicron strains. The leading nanobody (Nb), namely, Nb4, with excellent physicochemical properties, can neutralize Delta and Omicron subtypes, including BA.1, BA.1.1 (BA.1 + R346K), BA.2, BA.5, BQ.1, and XBB.1. The crystal structure of Nb4 in complex with the receptor-binding domain (RBD) of BA.1 Spike protein reveals that Nb4 interacts with an epitope on the RBD overlapping with the receptor-binding motif, and thus competes with angiotensin-converting enzyme 2 (ACE2) binding. Nb4 is expected to be effective for neutralizing most recent Omicron variants, since the epitopes are evolutionarily conserved among them. Indeed, trivalent Nb4 interacts with the XBB1.5 Spike protein with low nM affinity and competes for ACE2 binding. Prophylactic and therapeutic experiments in mice indicated that Nb4 could reduce the Omicron virus loads in the lung. In particular, in prophylactic experiments, intranasal administration of multivalent Nb4 completely protected mice from Omicron infection. Taken together, these results demonstrated that Nb4 could serve as a potent and broad-spectrum prophylactic and therapeutic Nb for COVID-19.
History
DepositionJul 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
D: Nanobody Nb4


Theoretical massNumber of molelcules
Total (without water)45,3882
Polymers45,3882
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.110, 76.110, 251.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Spike protein S1


Mass: 28329.930 Da / Num. of mol.: 1 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Details: Omicron BA.1
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody Nanobody Nb4


Mass: 17057.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium thiocyanate, 20 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 77.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.43→35.37 Å / Num. obs: 30440 / % possible obs: 100 % / Redundancy: 36.8 % / CC1/2: 0.997 / Net I/σ(I): 14.8
Reflection shellResolution: 2.43→2.49 Å / Num. unique obs: 828 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
AUTOMARdata reduction
xia2data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→35.37 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 3071 10.09 %
Rwork0.224 --
obs0.2286 30440 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 0 19 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.633
X-RAY DIFFRACTIONf_dihedral_angle_d4.77377
X-RAY DIFFRACTIONf_chiral_restr0.045387
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.470.39911410.34141214X-RAY DIFFRACTION98
2.47-2.510.34511320.3271228X-RAY DIFFRACTION97
2.51-2.550.35671430.32651239X-RAY DIFFRACTION97
2.55-2.60.36561350.321206X-RAY DIFFRACTION98
2.6-2.650.40351400.34621252X-RAY DIFFRACTION99
2.65-2.70.42791380.33571261X-RAY DIFFRACTION99
2.7-2.760.41621360.32961214X-RAY DIFFRACTION99
2.76-2.830.34851450.30531252X-RAY DIFFRACTION99
2.83-2.90.37621390.2741226X-RAY DIFFRACTION99
2.9-2.970.38811370.28531237X-RAY DIFFRACTION99
2.97-3.060.38541300.29121282X-RAY DIFFRACTION99
3.06-3.160.34491410.28211253X-RAY DIFFRACTION100
3.16-3.270.33861350.28891224X-RAY DIFFRACTION100
3.27-3.40.27071410.24741253X-RAY DIFFRACTION100
3.4-3.560.31221390.22221265X-RAY DIFFRACTION100
3.56-3.750.28451390.23251240X-RAY DIFFRACTION100
3.75-3.980.27821420.19621270X-RAY DIFFRACTION100
3.98-4.290.20261470.18841240X-RAY DIFFRACTION100
4.29-4.720.23631380.15821260X-RAY DIFFRACTION100
4.72-5.40.21521420.17611245X-RAY DIFFRACTION100
5.4-6.790.1771440.18821251X-RAY DIFFRACTION100
6.79-35.370.21551470.20261257X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.83892.2407-1.60082.0507-2.30093.5535-0.5634-0.2808-0.6747-0.7193-0.0308-0.60311.07550.48010.28620.90920.190.31750.36910.04560.911-25.304121.6487-3.5673
24.3588-0.4884-1.21871.81620.21171.1981-0.6449-0.0816-0.1682-0.26730.2840.21570.3253-0.13990.36180.8899-0.00430.00760.30340.06030.6676-56.966515.70939.8291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain E and resseq 334:527)
2X-RAY DIFFRACTION2(chain D and resseq -1:140)

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