6OU9

Asymmetric focused reconstruction of human norovirus GI.7 Houston strain VLP asymmetric unit in T=3 symmetry

• PDB DOI: https://doi.org/10.2210/pdb6OU9/pdb
• EM Map EMD-20198: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Norovirus Hu/GI.7/TCH-060/USA/2003
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-05-04 Released: 2019-06-26 
• Deposition Author(s): Jung, J., Grant, T., Thomas, D.R., Diehnelt, C.W., Grigorieff, N., Joshua-Tor, L.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.

Jung, J., Grant, T., Thomas, D.R., Diehnelt, C.W., Grigorieff, N., Joshua-Tor, L.

(2019) Proc Natl Acad Sci U S A 116: 12828-12832

• PubMed: 31182604 
• DOI: https://doi.org/10.1073/pnas.1903562116
• Primary Citation of Related Structures:  
  6OTF, 6OU9, 6OUC, 6OUT, 6OUU


• PubMed Abstract: 
  

  Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-Å) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn ²⁺ metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.

---

Organizational Affiliation: 

W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 174.3 kDa 
• Atom Count: 11,269 
• Modelled Residue Count: 1,473 
• Deposited Residue Count: 1,617 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A [auth B], B [auth A], C	539	Norovirus Hu/GI.7/TCH-060/USA/2003	Mutation(s): 0
UniProt
Find proteins for G8FL04 (Norovirus Hu/GI.7/TCH-060/USA/2003) Explore G8FL04  Go to UniProtKB:  G8FL04

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14
RECONSTRUCTION	cisTEM	1.0.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Jung, J., Grant, T., Thomas, D.R., Diehnelt, C.W., Grigorieff, N., Joshua-Tor, L.

---

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 2.0: 2019-11-20
  Changes: Advisory, Atomic model, Author supporting evidence, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Refinement description