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- PDB-7vnb: Crystal structure of the SARS-CoV-2 RBD in complex with a human s... -

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Basic information

Entry
Database: PDB / ID: 7vnb
TitleCrystal structure of the SARS-CoV-2 RBD in complex with a human single domain antibody n3113
Components
  • Spike protein S1
  • n3113
KeywordsVIRAL PROTEIN / SARS-CoV-2 / nanobody
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 / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsYang, Z. / Wang, Y. / Kong, Y. / Jin, Y. / Wu, Y. / Ying, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070938 China
CitationJournal: Signal Transduct Target Ther / Year: 2021
Title: A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants.
Authors: Zhenlin Yang / Yulu Wang / Yujia Jin / Yuanfei Zhu / Yanling Wu / Cheng Li / Yu Kong / Wenping Song / Xiaolong Tian / Wuqiang Zhan / Ailing Huang / Shanshan Zhou / Shuai Xia / Xiaoxu Tian / ...Authors: Zhenlin Yang / Yulu Wang / Yujia Jin / Yuanfei Zhu / Yanling Wu / Cheng Li / Yu Kong / Wenping Song / Xiaolong Tian / Wuqiang Zhan / Ailing Huang / Shanshan Zhou / Shuai Xia / Xiaoxu Tian / Chao Peng / Cuicui Chen / Yibing Shi / Gaowei Hu / Shujuan Du / Yuyan Wang / Youhua Xie / Shibo Jiang / Lu Lu / Lei Sun / Yuanlin Song / Tianlei Ying /
Abstract: The current COVID-19 pandemic has heavily burdened the global public health system and may keep simmering for years. The frequent emergence of immune escape variants have spurred the search for ...The current COVID-19 pandemic has heavily burdened the global public health system and may keep simmering for years. The frequent emergence of immune escape variants have spurred the search for prophylactic vaccines and therapeutic antibodies that confer broad protection against SARS-CoV-2 variants. Here we show that the bivalency of an affinity maturated fully human single-domain antibody (n3113.1-Fc) exhibits exquisite neutralizing potency against SARS-CoV-2 pseudovirus, and confers effective prophylactic and therapeutic protection against authentic SARS-CoV-2 in the host cell receptor angiotensin-converting enzyme 2 (ACE2) humanized mice. The crystal structure of n3113 in complex with the receptor-binding domain (RBD) of SARS-CoV-2, combined with the cryo-EM structures of n3113 and spike ecto-domain, reveals that n3113 binds to the side surface of up-state RBD with no competition with ACE2. The binding of n3113 to this novel epitope stabilizes spike in up-state conformations but inhibits SARS-CoV-2 S mediated membrane fusion, expanding our recognition of neutralization by antibodies against SARS-CoV-2. Binding assay and pseudovirus neutralization assay show no evasion of recently prevalent SARS-CoV-2 lineages, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) for n3113.1-Fc with Y58L mutation, demonstrating the potential of n3113.1-Fc (Y58L) as a promising candidate for clinical development to treat COVID-19.
History
DepositionOct 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: 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 23, 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
A: n3113
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1513
Polymers37,9292
Non-polymers2211
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-2 kcal/mol
Surface area15640 Å2
Unit cell
Length a, b, c (Å)146.210, 146.210, 93.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein n3113


Mass: 12963.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Spike protein S1


Mass: 24966.086 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: Spodoptera frugiperda (fall armyworm) / 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.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 5.05 Å3/Da / Density % sol: 75.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4.3M sodium chloride and 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→73.11 Å / Num. obs: 34264 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.1
Reflection shellResolution: 2.27→2.33 Å / Num. unique obs: 2535 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.15.2_3472refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.27→42.56 Å / SU ML: 0.2658 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.9074
RfactorNum. reflection% reflection
Rfree0.2033 1974 5.77 %
Rwork0.1767 32263 -
obs0.1783 34237 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.35 Å2
Refinement stepCycle: LAST / Resolution: 2.27→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 14 245 2859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762683
X-RAY DIFFRACTIONf_angle_d0.95443646
X-RAY DIFFRACTIONf_chiral_restr0.0559389
X-RAY DIFFRACTIONf_plane_restr0.0054472
X-RAY DIFFRACTIONf_dihedral_angle_d3.6841552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.28111090.28112350X-RAY DIFFRACTION99.8
2.33-2.390.35311170.26812332X-RAY DIFFRACTION99.55
2.39-2.460.28361510.25562245X-RAY DIFFRACTION99.63
2.46-2.540.23961480.242302X-RAY DIFFRACTION99.92
2.54-2.630.321550.23552329X-RAY DIFFRACTION99.96
2.63-2.740.25981470.21672285X-RAY DIFFRACTION99.88
2.74-2.860.24971610.20452275X-RAY DIFFRACTION99.96
2.86-3.010.23221170.19312343X-RAY DIFFRACTION99.92
3.01-3.20.21321160.1872342X-RAY DIFFRACTION99.92
3.2-3.450.19841360.16572293X-RAY DIFFRACTION99.96
3.45-3.790.17961840.14652262X-RAY DIFFRACTION100
3.79-4.340.16141750.12882285X-RAY DIFFRACTION99.96
4.34-5.470.14011280.13372320X-RAY DIFFRACTION99.96
5.47-42.530.20391300.18072300X-RAY DIFFRACTION99.1

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