8VLT

Crystal structure of glycan-targeting antibody 2526 Fab bound to Mannose

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

  • Deposited: 2024-01-12 Released: 2024-10-16 
  • Deposition Author(s): Lindenberger, J., Acharya, P.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Literature

Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families.

Vukovich, M.J.Shiakolas, A.R.Lindenberger, J.Richardson, R.A.Bass, L.E.Barr, M.Liu, Y.Go, E.P.Park, C.S.May, A.J.Sammour, S.Kambarami, C.Huang, X.Janowska, K.Edwards, R.J.Mansouri, K.Spence, T.N.Abu-Shmais, A.A.Manamela, N.P.Richardson, S.I.Leonard, S.E.W.Gripenstraw, K.R.Setliff, I.Saunders, K.O.Bonami, R.H.Ross, T.M.Desaire, H.Moore, P.L.Parks, R.Haynes, B.F.Sheward, D.J.Acharya, P.Sautto, G.A.Georgiev, I.S.

(2024) PLoS Pathog 20: e1012499-e1012499

  • DOI: https://doi.org/10.1371/journal.ppat.1012499
  • Primary Citation of Related Structures:  
    8VLT

  • PubMed Abstract: 

    Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage members, antibodies 2526 and 546, were confirmed to bind to a large panel of diverse antigens, including several strains of HIV-1 Env, influenza HA, coronavirus (CoV) spike, hepatitis C virus (HCV) E protein, Nipah virus (NiV) F protein, and Langya virus (LayV) F protein. We found that both antibodies bind to complex glycans on the antigenic surfaces. Antibody 2526 targets the stem region of influenza HA and the N-terminal domain (NTD) region of SARS-CoV-2 spike. A crystal structure of 2526 Fab bound to mannose revealed the presence of a glycan-binding pocket on the light chain. Antibody 2526 cross-reacted with antigens from multiple pathogens and displayed no signs of autoreactivity. These features distinguish antibody 2526 from previously described glycan-reactive antibodies. Further study of this antibody class may aid in the selection and engineering of broadly reactive antibody therapeutics and can inform the development of effective vaccines with exceptional breadth of pathogen coverage.


  • Organizational Affiliation

    Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2526 Fab Heavy ChainA [auth H]222Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2526 Fab Light ChainB [auth L]219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
C [auth L]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.49α = 90
b = 68.49β = 90
c = 97.341γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI165147
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI170752

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release