8DWA

Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.

Luo, M.Zhou, B.Reddem, E.R.Tang, B.Chen, B.Zhou, R.Liu, H.Liu, L.Katsamba, P.S.Au, K.K.Man, H.O.To, K.K.Yuen, K.Y.Shapiro, L.Dang, S.Ho, D.D.Chen, Z.

(2023) Emerg Microbes Infect 12: 2146538-2146538

  • DOI: https://doi.org/10.1080/22221751.2022.2146538
  • Primary Citation of Related Structures:  
    7YKJ, 8DW9, 8DWA, 8DXS

  • PubMed Abstract: 

    ABSTRACT Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.


  • Organizational Affiliation

    AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1181Severe 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P1D9 Heavy chainB [auth H]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
P1D9 Light chainC [auth L]211Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.136α = 90
b = 147.136β = 90
c = 80.108γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Jack Ma FoundationChina--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary