Virus-like particle of bacteriophage ESE058

Experimental Data Snapshot

  • Resolution: 3.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.

Rumnieks, J.Lieknina, I.Kalnins, G.Sisovs, M.Akopjana, I.Bogans, J.Tars, K.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abc0023
  • Primary Citation of Related Structures:  
    6YF7, 6YF9, 6YFA, 6YFB, 6YFC, 6YFD, 6YFE, 6YFF, 6YFG, 6YFH, 6YFI, 6YFJ, 6YFK, 6YFL, 6YFM, 6YFN, 6YFO, 6YFP, 6YFQ, 6YFR, 6YFS, 6YFT, 6YFU

  • PubMed Abstract: 

    The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.

  • Organizational Affiliation

    Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein146Leviviridae sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
AD [auth BD]
CD [auth BG]
DD [auth BG]
ED [auth BJ]
AD [auth BD],
CD [auth BG],
DD [auth BG],
ED [auth BJ],
FD [auth BM],
GD [auth BM],
HD [auth BP],
ID [auth BP],
JD [auth BS],
KD [auth BS],
LD [auth BV],
MC [auth AC],
MD [auth BV],
NC [auth AC],
ND [auth BY],
OC [auth AF],
OD [auth BY],
PC [auth AF],
PD [auth CE],
QC [auth AI],
RC [auth AL],
SC [auth AO],
TC [auth AO],
UC [auth AR],
VC [auth AU],
WC [auth AU],
XC [auth AX],
YC [auth BA],
ZC [auth BA]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 500.893α = 90
b = 500.893β = 90
c = 287.055γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Regional Development FundLatvia1.1.1.1/16/A/104

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description