7C8W

Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection.

Li, T.Cai, H.Yao, H.Zhou, B.Zhang, N.van Vlissingen, M.F.Kuiken, T.Han, W.GeurtsvanKessel, C.H.Gong, Y.Zhao, Y.Shen, Q.Qin, W.Tian, X.X.Peng, C.Lai, Y.Wang, Y.Hutter, C.A.J.Kuo, S.M.Bao, J.Liu, C.Wang, Y.Richard, A.S.Raoul, H.Lan, J.Seeger, M.A.Cong, Y.Rockx, B.Wong, G.Bi, Y.Lavillette, D.Li, D.

(2021) Nat Commun 12: 4635-4635

  • DOI: 10.1038/s41467-021-24905-z
  • Primary Citation of Related Structures:  
    7C8V, 7C8W, 7CAN

  • PubMed Abstract: 
  • SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1-6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics 7-17 ...

    SARS-CoV-2, the causative agent of COVID-19 1 , features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein 1-6 . Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics 7-17 . Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K D  = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC 50  = 0.42 μg mL -1 ). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log 10 . Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.


    Organizational Affiliation

    State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China. dianfan.li@sibcb.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Synthetic nanobody MR17A122synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1B213Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G63564LA
GlyCosmos:  G63564LA
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.691α = 90
b = 73.691β = 90
c = 158.577γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31870726
Chinese Academy of SciencesChinaQYZDB-SSW-SMC037
Chinese Academy of SciencesChinaXDB37020204

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-03-10
    Changes: Structure summary
  • Version 2.2: 2022-01-05
    Changes: Database references