27ZD | pdb_000027zd

Human norovirus GII.3 TCH04-577 VP1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 27ZD

This is version 1.0 of the entry. See complete history

Literature

Conformational Plasticity of the Human Norovirus GII.3 Capsid Reveals Alternative P Domain Interaction Networks.

Song, C.Miki, M.Takai-Todaka, R.Murakami, K.Katayama, K.Murata, K.

(2026) Int J Mol Sci 27

  • DOI: https://doi.org/10.3390/ijms27156586
  • Primary Citation Related Structures: 
    27ZD

  • PubMed Abstract: 

    Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide, yet no effective antiviral therapeutics are currently available. Although environmentally induced capsid conformational changes associated with infectivity have been reported in murine noroviruses (MNVs), comparable conformational switching has not been demonstrated in HuNoVs. In this study, we generated HuNoV GII.3 virus-like particles (VLPs) using a baculovirus expression system and identified two distinct T = 3 particle populations coexisting within VLP preparations derived from a single strain through cryo-electron microscopy single-particle analysis. Comparative structural analysis revealed that these two T = 3 capsid conformations correspond to the resting and rising states of the protruding (P) domain. Rearrangement of the P domain alters intermolecular interactions between adjacent capsid subunits, resulting in distinct capsid surface architectures. In the resting state, intermolecular contacts were mediated predominantly by the P2 subdomain, with limited contribution from the P1 subdomain. In contrast, the rising state exhibited a shift toward an alternative interaction interface primarily involving the P1 subdomain. The alteration of the capsid surface accompanying this conformational switching can influence biologically relevant intermolecular interactions with viral hosts and antibodies as demonstrated in murine norovirus. These findings demonstrate previously unrecognized structural polymorphism in the HuNoV capsid and provide evidence that conformational switching may occur in HuNoVs. Our results offer new insights into norovirus capsid dynamics and may inform future structure-based vaccine and antiviral drug development.


  • Organizational Affiliation
    • Department of Convergence Medicine, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 180.32 kDa 
  • Atom Count: 11,951 
  • Modeled Residue Count: 1,541 
  • Deposited Residue Count: 1,644 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Human norovirus GII.3 TCH04-577 VP1
A, B, C
548Norovirus Hu/Texas/TCH04-577/2004/USMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00440289
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2026-25476185
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121005
Japan Agency for Medical Research and Development (AMED)JapanJP25ama121005

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release