6HCN

Adenovirus Type 5 Fiber Knob protein at 1.49A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/s41467-019-08599-y
  • Primary Citation of Related Structures:  

  • 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 platfor ...

    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. ParkerAL@Cardiff.ac.uk.,Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.,Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA.,Immunocore Ltd., Abingdon, OX14 4RY, Oxon, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fiber protein
A, C
186Human adenovirus C serotype 5Mutation(s): 0 
Find proteins for P11818 (Human adenovirus C serotype 5)
Go to UniProtKB:  P11818
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fiber protein
B
188Human adenovirus C serotype 5Mutation(s): 0 
Find proteins for P11818 (Human adenovirus C serotype 5)
Go to UniProtKB:  P11818
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 102.160α = 90.00
b = 102.440β = 90.00
c = 77.010γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references