Adenovirus species 48, fiber knob protein

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Diversity within the adenovirus fiber knob hypervariable loops influences primary receptor interactions.

Baker, A.T.Greenshields-Watson, A.Coughlan, L.Davies, J.A.Uusi-Kerttula, H.Cole, D.K.Rizkallah, P.J.Parker, A.L.

(2019) Nat Commun 10: 741-741

  • DOI: https://doi.org/10.1038/s41467-019-08599-y
  • Primary Citation of Related Structures:  
    6FJN, 6FJQ, 6HCN

  • PubMed Abstract: 

    Adenovirus based vectors are of increasing importance for wide ranging therapeutic applications. As vaccines, vectors derived from human adenovirus species D serotypes 26 and 48 (HAdV-D26/48) are demonstrating promising efficacy as protective platforms against infectious diseases. Significant clinical progress has been made, yet definitive studies underpinning mechanisms of entry, infection, and receptor usage are currently lacking. Here, we perform structural and biological analysis of the receptor binding fiber-knob protein of HAdV-D26/48, reporting crystal structures, and modelling putative interactions with two previously suggested attachment receptors, CD46 and Coxsackie and Adenovirus Receptor (CAR). We provide evidence of a low affinity interaction with CAR, with modelling suggesting affinity is attenuated through extended, semi-flexible loop structures, providing steric hindrance. Conversely, in silico and in vitro experiments are unable to provide evidence of interaction between HAdV-D26/48 fiber-knob with CD46, or with Desmoglein 2. Our findings provide insight into the cell-virus interactions of HAdV-D26/48, with important implications for the design and engineering of optimised Ad-based therapeutics.

  • Organizational Affiliation

    Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
195Human adenovirus 48Mutation(s): 0 
Find proteins for A4ZKK6 (Human adenovirus 48)
Explore A4ZKK6 
Go to UniProtKB:  A4ZKK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZKK6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B],
H [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.91 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.205α = 90
b = 145.205β = 90
c = 145.205γ = 90
Software Package:
Software NamePurpose
xia2data reduction
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description