7RD1 image
Deposition Date 2021-07-08
Release Date 2021-12-15
Last Version Date 2024-06-05
Entry Detail
PDB ID:
7RD1
Keywords:
Title:
The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.07 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Pre-protein VI
Gene (Uniprot):L3
Chain IDs:A (auth: 0), B (auth: U), C (auth: 1), D (auth: V), E (auth: 2), F (auth: W), G (auth: 3), H (auth: X), I (auth: 4), J (auth: Y), K (auth: 8), L (auth: Z)
Chain Length:243
Number of Molecules:12
Biological Source:Chimpanzee adenovirus Y25
Polymer Type:polypeptide(L)
Molecule:Hexon protein
Gene (Uniprot):L3
Chain IDs:M (auth: A), N (auth: B), O (auth: C), P (auth: D), Q (auth: E), R (auth: F), S (auth: G), T (auth: H), U (auth: I), V (auth: J), W (auth: K), X (auth: L)
Chain Length:942
Number of Molecules:12
Biological Source:Chimpanzee adenovirus Y25
Polymer Type:polypeptide(L)
Molecule:Penton protein
Gene (Uniprot):L2
Chain IDs:Y (auth: M)
Chain Length:532
Number of Molecules:1
Biological Source:Chimpanzee adenovirus Y25
Polymer Type:polypeptide(L)
Molecule:Hexon-interlacing protein
Gene (Uniprot):IX
Chain IDs:Z (auth: N), AA (auth: O), BA (auth: P), CA (auth: Q)
Chain Length:142
Number of Molecules:4
Biological Source:Chimpanzee adenovirus Y25
Polymer Type:polypeptide(L)
Molecule:Pre-hexon-linking protein IIIa
Chain IDs:DA (auth: R)
Chain Length:589
Number of Molecules:1
Biological Source:Chimpanzee adenovirus Y25
Polymer Type:polypeptide(L)
Molecule:Pre-hexon-linking protein VIII
Gene (Uniprot):L4
Chain IDs:EA (auth: S), FA (auth: T)
Chain Length:227
Number of Molecules:2
Biological Source:Chimpanzee adenovirus Y25
Ligand Molecules
Primary Citation

Abstact

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.

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Protein

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Disease

Primary Citation of related structures