9DBT | pdb_00009dbt

Crystal structure of human astrovirus 1 capsid spike bound to human neonatal Fc receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.263 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure of the human astrovirus capsid spike in complex with the neonatal Fc receptor.

Lentz, A.Lanning, S.Iranpur, K.R.Ricemeyer, L.Arias, C.F.DuBois, R.M.

(2025) Nat Commun 16: 9621-9621

  • DOI: https://doi.org/10.1038/s41467-025-65203-2
  • Primary Citation of Related Structures:  
    9DBT

  • PubMed Abstract: 

    Human astroviruses (HAstVs) are a leading cause of viral gastroenteritis in children worldwide. Recently the neonatal Fc receptor (FcRn) was identified as a receptor for HAstV, however the molecular basis for the FcRn-HAstV interaction remained unclear. Here, we report the crystal structure of FcRn bound to the HAstV capsid spike domain at 3.4 angstroms resolution. We show that all classical HAstV spikes bind to FcRn and we identify three conserved HAstV spike residues that mediate binding to FcRn. Using competition binding assays, we show that the HAstV spike competes with IgG for binding to FcRn. Additionally, we demonstrate that the FcRn inhibitor, nipocalimab, and anti-HAstV neutralizing monoclonal antibodies block HAstV spike binding to FcRn, revealing their neutralization mechanisms and supporting their therapeutic potential. Overall, our findings illuminate a crucial interaction in the HAstV life cycle, which may help to inform the development of a HAstV vaccine and antibody therapies.


  • Organizational Affiliation
    • Department of Microbiology & Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51A,
C [auth F],
E [auth I],
J [auth C]
278Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
PHAROS:  P55899
GTEx:  ENSG00000104870 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55899
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
D [auth G],
F [auth J],
K [auth D]
99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
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UniProt GroupP61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Structural proteinG [auth H],
H [auth K],
I [auth L],
L [auth E]
228Human astrovirus 1Mutation(s): 0 
UniProt
Find proteins for O12792 (Human astrovirus-1)
Explore O12792 
Go to UniProtKB:  O12792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO12792
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.263 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87α = 90
b = 152.999β = 90
c = 255.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing

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: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references