8OFU

Human adenovirus type 53 fiber-knob protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Broad sialic acid usage amongst species D human adenovirus.

Mundy, R.M.Baker, A.T.Bates, E.A.Cunliffe, T.G.Teijeira-Crespo, A.Moses, E.Rizkallah, P.J.Parker, A.L.

(2023) Npj Viruses 1: 1-1

  • DOI: https://doi.org/10.1038/s44298-023-00001-5
  • Primary Citation of Related Structures:  
    8OFP, 8OFQ, 8OFR, 8OFS, 8OFT, 8OFU, 8OFV

  • PubMed Abstract: 

    Human adenoviruses (HAdV) are widespread pathogens causing usually mild infections. The Species D (HAdV-D) cause gastrointestinal tract infections and epidemic keratoconjunctivitis (EKC). Despite being significant pathogens, knowledge around HAdV-D mechanism of cell infection is lacking. Sialic acid (SA) usage has been proposed as a cell infection mechanism for EKC causing HAdV-D. Here we highlight an important role for SA engagement by many HAdV-D. We provide apo state crystal structures of 7 previously undetermined HAdV-D fiber-knob proteins, and structures of HAdV-D25, D29, D30 and D53 fiber-knob proteins in complex with SA. Biologically, we demonstrate that removal of cell surface SA reduced infectivity of HAdV-C5 vectors pseudotyped with HAdV-D fiber-knob proteins, whilst engagement of the classical HAdV receptor CAR was variable. Our data indicates variable usage of SA and CAR across HAdV-D. Better defining these interactions will enable improved development of antivirals and engineering of the viruses into refined therapeutic vectors.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber protein
A, B, C, D, E
A, B, C, D, E, F
188Human adenovirus 53Mutation(s): 0 
Gene Names: L5
UniProt
Find proteins for E5RWD1 (Human adenovirus 53)
Explore E5RWD1 
Go to UniProtKB:  E5RWD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5RWD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth D],
MA [auth F],
NA [auth F],
W [auth C],
X [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth E]
G [auth A]
H [auth A]
JA [auth F]
KA [auth F]
FA [auth E],
G [auth A],
H [auth A],
JA [auth F],
KA [auth F],
N [auth B],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
GA [auth E]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
K [auth A],
L [auth A],
LA [auth F],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.314α = 90
b = 60.526β = 91.8
c = 93.837γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N0137941/1
Wellcome TrustUnited Kingdom517732

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary