7AJP

Crystal Structure of Human Adenovirus 56 Fiber Knob


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46.

Persson, B.D.John, L.Rafie, K.Strebl, M.Frangsmyr, L.Ballmann, M.Z.Mindler, K.Havenga, M.Lemckert, A.Stehle, T.Carlson, L.A.Arnberg, N.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2020732118
  • Primary Citation of Related Structures:  
    7AJP

  • PubMed Abstract: 
  • Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID-19) and other severe infectious diseases. The efficacy of such vector-based vaccines depends on functional interactions with receptors on host cells ...

    Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID-19) and other severe infectious diseases. The efficacy of such vector-based vaccines depends on functional interactions with receptors on host cells. Adenoviruses of different species are assumed to enter host cells mainly by interactions between the knob domain of the protruding fiber capsid protein and cellular receptors. Using a cell-based receptor-screening assay, we identified CD46 as a receptor for HAdV-D56. The function of CD46 was validated in infection experiments using cells lacking and overexpressing CD46, and by competition infection experiments using soluble CD46. Remarkably, unlike HAdV-B types that engage CD46 through interactions with the knob domain of the fiber protein, HAdV-D types infect host cells through a direct interaction between CD46 and the hexon protein. Soluble hexon proteins (but not fiber knob) inhibited HAdV-D56 infection, and surface plasmon analyses demonstrated that CD46 binds to HAdV-D hexon (but not fiber knob) proteins. Cryoelectron microscopy analysis of the HAdV-D56 virion-CD46 complex confirmed the interaction and showed that CD46 binds to the central cavity of hexon trimers. Finally, soluble CD46 inhibited infection by 16 out of 17 investigated HAdV-D types, suggesting that CD46 is an important receptor for a large group of adenoviruses. In conclusion, this study identifies a noncanonical entry mechanism used by human adenoviruses, which adds to the knowledge of adenovirus biology and can also be useful for development of adenovirus-based vaccine vectors.


    Organizational Affiliation

    Laboratory for Molecular Infection Medicine Sweden, Umeå University, SE-90185 Umeå, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fiber
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
208Human adenovirus 56Mutation(s): 0 
UniProt
Find proteins for R9RU05 (Human adenovirus 56)
Explore R9RU05 
Go to UniProtKB:  R9RU05
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
KA [auth C], RA [auth D], UB [auth L], X [auth A], ZA [auth E]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth F] , CB [auth G] , DB [auth G] , FA [auth C] , FB [auth H] , GA [auth C] , LA [auth D] , LB [auth I] , 
AB [auth F], CB [auth G], DB [auth G], FA [auth C], FB [auth H], GA [auth C], LA [auth D], LB [auth I], M [auth A], MB [auth I], N [auth A], NB [auth I], QB [auth J], RB [auth J], SA [auth E], SB [auth K], TB [auth L], Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , BB [auth F] , CA [auth B] , DA [auth B] , EA [auth B] , EB [auth G] , GB [auth H] , 
AA [auth B], BA [auth B], BB [auth F], CA [auth B], DA [auth B], EA [auth B], EB [auth G], GB [auth H], HA [auth C], HB [auth H], IA [auth C], IB [auth H], JA [auth C], JB [auth H], KB [auth H], NA [auth D], OA [auth D], OB [auth I], P [auth A], PA [auth D], PB [auth I], Q [auth A], QA [auth D], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], VA [auth E], W [auth A], WA [auth E], XA [auth E], YA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
MA [auth D], O [auth A], TA [auth E], UA [auth E], Z [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.443α = 90
b = 182.529β = 118.541
c = 117.029γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Baden-Wuerttemberg-StiftungGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release