9CBN | pdb_00009cbn

HAstV1 spike in complex with neutralizing Fabs 3H4 and 3B4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of three novel neutralizing antibody epitopes on the human astrovirus capsid spike and mechanistic insights into virus neutralization.

Lanning, S.Aguilar-Hernandez, N.Serrao, V.H.B.Lopez, T.O'Rourke, S.M.Lentz, A.Ricemeyer, L.Espinosa, R.Lopez, S.Arias, C.F.DuBois, R.M.

(2025) J Virol 99: e0161924-e0161924

  • DOI: https://doi.org/10.1128/jvi.01619-24
  • Primary Citation of Related Structures:  
    9CBN, 9CN2

  • PubMed Abstract: 

    Human astroviruses (HAstVs) are a leading cause of viral childhood diarrhea that infects nearly every individual during their lifetime. Although human astroviruses are highly prevalent, no approved vaccine currently exists. Antibody responses appear to play an important role in protection from HAstV infection; however, knowledge about the neutralizing epitope landscape is lacking, as only three neutralizing antibody epitopes have previously been determined. Here, we structurally define the epitopes of three uncharacterized HAstV-neutralizing monoclonal antibodies: antibody 4B6 with X-ray crystallography to 2.67 Å, and antibodies 3H4 and 3B4 simultaneously with single-particle cryogenic-electron microscopy to 3.33 Å. We assess the epitope locations relative to conserved regions on the capsid spike and find that while antibodies 4B6 and 3B4 target the upper variable loop regions of the HAstV spike protein, antibody 3H4 targets a novel region near the base of the spike that is more conserved. Additionally, we found that all three antibodies bind with high affinity, and they compete with receptor FcRn binding to the capsid spike. These studies inform which regions of the HAstV capsid can be targeted by monoclonal antibody therapies and could aid in rational vaccine design.IMPORTANCEHuman astroviruses (HAstVs) infect nearly every child in the world, causing diarrhea, vomiting, and fever. Despite the prevalence of human astroviruses, little is known about how antibodies block virus infection. Here, we determined high-resolution structures of the astrovirus capsid protein in a complex with three virus-neutralizing antibodies. The antibodies bind distinct sites on the capsid spike domain. The antibodies block virus attachment to human cells and prevent capsid spike interaction with the human neonatal Fc receptor. These findings support the use of the human astrovirus capsid spike as an antigen in a vaccine to prevent astrovirus disease.


  • Organizational Affiliation
    • Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HAstV1 neutralizing Fab 3B4 heavy chain225Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HAstV1 neutralizing Fab 3B4 kappa chain214Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein
C, D
228Human astrovirus 1Mutation(s): 0 
UniProt
Find proteins for O12792 (Human astrovirus-1)
Explore O12792 
Go to UniProtKB:  O12792
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UniProt GroupO12792
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HAstV1 neutralizing Fab 3H4 heavy chain
E, G
228Mus musculusMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
HAstV1 neutralizing Fab 3H4 lambda chain
F, H
217Mus musculusMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI144090

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references