6N8D | pdb_00006n8d

Crystal structure of GII.4 2002 norovirus P domain in complex with neutralizing human antibody A1431

• PDB DOI: https://doi.org/10.2210/pdb6N8D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Norovirus Hu/GII.4/Farmington Hills/2004/USA, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2018-11-29 Released: 2019-06-19 
• Deposition Author(s): Changela, A., Verardi, R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Models: experimental

Literature

Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination.

Lindesmith, L.C., McDaniel, J.R., Changela, A., Verardi, R., Kerr, S.A., Costantini, V., Brewer-Jensen, P.D., Mallory, M.L., Voss, W.N., Boutz, D.R., Blazeck, J.J., Ippolito, G.C., Vinje, J., Kwong, P.D., Georgiou, G., Baric, R.S.

(2019) Immunity 50: 1530-1541.e8

• PubMed: 31216462 
• DOI: https://doi.org/10.1016/j.immuni.2019.05.007
• Primary Citation Related Structures: 
  6N81, 6N8D


• PubMed Abstract: 
  

  Rapidly evolving RNA viruses, such as the GII.4 strain of human norovirus (HuNoV), and their vaccines elicit complex serological responses associated with previous exposure. Specific correlates of protection, moreover, remain poorly understood. Here, we report the GII.4-serological antibody repertoire-pre- and post-vaccination-and select several antibody clonotypes for epitope and structural analysis. The humoral response was dominated by GII.4-specific antibodies that blocked ancestral strains or by antibodies that bound to divergent genotypes and did not block viral-entry-ligand interactions. However, one antibody, A1431, showed broad blockade toward tested GII.4 strains and neutralized the pandemic GII.P16-GII.4 Sydney strain. Structural mapping revealed conserved epitopes, which were occluded on the virion or partially exposed, allowing for broad blockade with neutralizing activity. Overall, our results provide high-resolution molecular information on humoral immune responses after HuNoV vaccination and demonstrate that infection-derived and vaccine-elicited antibodies can exhibit broad blockade and neutralization against this prevalent human pathogen.

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Organizational Affiliation: 
• Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: [e-mail].
Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 164.78 kDa 
• Atom Count: 11,214 
• Modeled Residue Count: 1,468 
• Deposited Residue Count: 1,524 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A [auth C], D [auth A]	309	Norovirus Hu/GII.4/Farmington Hills/2004/USA	Mutation(s): 0
UniProt
Find proteins for R4I4P2 (Norovirus Hu/GII.4/Farmington Hills/2004/USA) Explore R4I4P2  Go to UniProtKB:  R4I4P2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A1431 Fab light chain	B [auth E], E [auth B]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A1431 Fab heavy chain	C [auth F], F [auth D]	238	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.369	α = 90
b = 157.356	β = 112.93
c = 110.362	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Changela, A., Verardi, R., Kwong, P.D.

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary