7LK9

Crystal structure of SARS-CoV-2 RBD-targeting antibody COV107-23 HC + COVD21-C8 LC

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-02-01 Released: 2021-02-17 
  • Deposition Author(s): Yuan, M., Zhu, X., Wilson, I.A., Wu, N.C.
  • Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sequence signatures of two IGHV3-53/3-66 public clonotypes to SARS-CoV-2 receptor binding domain.

Tan, T.J.C.Yuan, M.Kuzelka, K.Padron, G.C.Beal, J.R.Chen, X.Wang, Y.Rivera-Cardona, J.Zhu, X.Stadtmueller, B.M.Brooke, C.B.Wilson, I.A.Wu, N.C.

(2021) Biorxiv 

  • DOI: 10.1101/2021.01.26.428356
  • Primary Citation of Related Structures:  
    7LK9, 7LKA

  • PubMed Abstract: 
  • Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short CDR H3. Germline-encoded sequence motifs in CDRs H1 and H2 play a major role, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, have not been elucidated ...

    Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short CDR H3. Germline-encoded sequence motifs in CDRs H1 and H2 play a major role, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, have not been elucidated. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that appear to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. Overall, our results advance fundamental understanding of the antibody response to SARS-CoV-2.


    Organizational Affiliation

    Photobiotechnology, Department of Plant Biochemistry, Ruhr-Universität Bochum, 44801, Bochum, Germany. thomas.happe@rub.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COV107-23 heavy chainC [auth A], E [auth C], A [auth H], G [auth M]220Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COVD21-C8 light chainD [auth B], F [auth D], B [auth L], H [auth N]216Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.297α = 100.12
b = 78.383β = 112.09
c = 91.626γ = 92.8
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR00 AI139445

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references