The crystal structure of Penaeus vannamei nodavirus P-domain (P212121)

Experimental Data Snapshot

  • Resolution: 1.22 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.

Chen, N.C.Yoshimura, M.Miyazaki, N.Guan, H.H.Chuankhayan, P.Lin, C.C.Chen, S.K.Lin, P.J.Huang, Y.C.Iwasaki, K.Nakagawa, A.Chan, S.I.Chen, C.J.

(2019) Commun Biol 2: 72-72

  • DOI: https://doi.org/10.1038/s42003-019-0311-z
  • Primary Citation of Related Structures:  
    5YKU, 5YKV, 5YKX, 5YKZ, 5YL0, 5YL1, 6AB5, 6AB6

  • PubMed Abstract: 

    Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T  = 3 and T  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T  = 3 and T  = 1 assemblies. Increasing the N / C -termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.

  • Organizational Affiliation

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D
119Penaeus vannamei nodavirusMutation(s): 0 
Find proteins for A5H7Q8 (Penaeus vannamei nodavirus)
Explore A5H7Q8 
Go to UniProtKB:  A5H7Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H7Q8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.22 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.843α = 90
b = 69.736β = 90
c = 146.606γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwan105-2311-B-213-001-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references