7RD1

The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-protein VI243Chimpanzee adenovirus Y25Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for G9G853 (Chimpanzee adenovirus Y25)
Explore G9G853 
Go to UniProtKB:  G9G853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9G853
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hexon protein942Chimpanzee adenovirus Y25Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for G9G854 (Chimpanzee adenovirus Y25)
Explore G9G854 
Go to UniProtKB:  G9G854
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UniProt GroupG9G854
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Penton proteinY [auth M]532Chimpanzee adenovirus Y25Mutation(s): 0 
Gene Names: L2
UniProt
Find proteins for G9G849 (Chimpanzee adenovirus Y25)
Explore G9G849 
Go to UniProtKB:  G9G849
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UniProt GroupG9G849
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hexon-interlacing proteinAA [auth O],
BA [auth P],
CA [auth Q],
Z [auth N]
142Chimpanzee adenovirus Y25Mutation(s): 0 
Gene Names: IX
UniProt
Find proteins for G9G843 (Chimpanzee adenovirus Y25)
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UniProt GroupG9G843
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-hexon-linking protein IIIaDA [auth R]589Chimpanzee adenovirus Y25Mutation(s): 0 
UniProt
Find proteins for G9G848 (Chimpanzee adenovirus Y25)
Explore G9G848 
Go to UniProtKB:  G9G848
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UniProt GroupG9G848
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-hexon-linking protein VIIIEA [auth S],
FA [auth T]
227Chimpanzee adenovirus Y25Mutation(s): 0 
Gene Names: L4
UniProt
Find proteins for G9G860 (Chimpanzee adenovirus Y25)
Explore G9G860 
Go to UniProtKB:  G9G860
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UniProt GroupG9G860
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.1
MODEL REFINEMENTMDFF
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1531991

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release