7OP2

Chadox1/ Chimpanzee adenovirus Y25 fiber knob protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome.

Baker, A.T.Boyd, R.J.Sarkar, D.Teijeira-Crespo, A.Chan, C.K.Bates, E.Waraich, K.Vant, J.Wilson, E.Truong, C.D.Lipka-Lloyd, M.Fromme, P.Vermaas, J.Williams, D.Machiesky, L.Heurich, M.Nagalo, B.M.Coughlan, L.Umlauf, S.Chiu, P.L.Rizkallah, P.J.Cohen, T.S.Parker, A.L.Singharoy, A.Borad, M.J.

(2021) Sci Adv 7: eabl8213-eabl8213

  • DOI: https://doi.org/10.1126/sciadv.abl8213
  • Primary Citation of Related Structures:  
    7OP2, 7RD1

  • PubMed Abstract: 

    Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.


  • Organizational Affiliation

    Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
187Chimpanzee adenovirus Y25Mutation(s): 0 
UniProt
Find proteins for G9G864 (Chimpanzee adenovirus Y25)
Explore G9G864 
Go to UniProtKB:  G9G864
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9G864
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
S [auth D],
T [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth H]
CA [auth H]
DA [auth H]
EA [auth I]
AA [auth G],
BA [auth H],
CA [auth H],
DA [auth H],
EA [auth I],
FA [auth I],
GA [auth J],
HA [auth J],
IA [auth K],
JA [auth L],
KA [auth L],
N [auth A],
O [auth C],
R [auth D],
U [auth E],
V [auth F],
X [auth G],
Y [auth G],
Z [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth A],
P [auth D],
Q [auth D],
W [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.427α = 90
b = 112.26β = 92.61
c = 98.605γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
DIALSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description