3ONY

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with Fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability.

Hansman, G.S.Biertumpfel, C.Georgiev, I.McLellan, J.S.Chen, L.Zhou, T.Katayama, K.Kwong, P.D.

(2011) J Virol 85: 6687-6701

  • DOI: https://doi.org/10.1128/JVI.00246-11
  • Primary Citation of Related Structures:  
    3ONU, 3ONY, 3PA1, 3PA2, 3Q38, 3Q39, 3Q3A, 3Q6Q, 3Q6R, 3R6J, 3R6K

  • PubMed Abstract: 

    Noroviruses are the dominant cause of outbreaks of gastroenteritis worldwide, and interactions with human histo-blood group antigens (HBGAs) are thought to play a critical role in their entry mechanism. Structures of noroviruses from genogroups GI and GII in complex with HBGAs, however, reveal different modes of interaction. To gain insight into norovirus recognition of HBGAs, we determined crystal structures of norovirus protruding domains from two rarely detected GII genotypes, GII.10 and GII.12, alone and in complex with a panel of HBGAs, and analyzed structure-function implications related to conservation of the HBGA binding pocket. The GII.10- and GII.12-apo structures as well as the previously solved GII.4-apo structure resembled each other more closely than the GI.1-derived structure, and all three GII structures showed similar modes of HBGA recognition. The primary GII norovirus-HBGA interaction involved six hydrogen bonds between a terminal αfucose1-2 of the HBGAs and a dimeric capsid interface, which was composed of elements from two protruding subdomains. Norovirus interactions with other saccharide units of the HBGAs were variable and involved fewer hydrogen bonds. Sequence analysis revealed a site of GII norovirus sequence conservation to reside under the critical αfucose1-2 and to be one of the few patches of conserved residues on the outer virion-capsid surface. The site was smaller than that involved in full HBGA recognition, a consequence of variable recognition of peripheral saccharides. Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus.


  • Organizational Affiliation

    Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, 40 Convent Drive, Building 40, Room 4508, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C
318Norwalk virusMutation(s): 0 
UniProt
Find proteins for Q5F4T5 (Norwalk virus)
Explore Q5F4T5 
Go to UniProtKB:  Q5F4T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5F4T5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
O [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.529α = 90
b = 115.905β = 90
c = 267.801γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary