9CLI

Cryo-EM model derived from localized reconstruction of human adenovirus (Ad5)-hexon-FX complex at 3.6A resolution

  • Classification: VIRUS
  • Organism(s): Human adenovirus 5, Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-07-11 Released: 2024-11-27 
  • Deposition Author(s): Reddy, V.S., Ma, O.X.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-derived insights from blood factors binding to the surfaces of different adenoviruses.

Mudrick, H.E.Lu, S.C.Bhandari, J.Barry, M.E.Hemsath, J.R.Andres, F.G.M.Ma, O.X.Barry, M.A.Reddy, V.S.

(2024) Nat Commun 15: 9768-9768

  • DOI: https://doi.org/10.1038/s41467-024-54049-9
  • Primary Citation of Related Structures:  
    9CLI, 9CLN, 9CLS, 9CM2, 9CM9, 9CMO

  • PubMed Abstract: 

    The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of several human adenoviruses with human platelet factor-4 (PF4), coagulation factors FII (Prothrombin), and FX. While we observed EM densities for FII and FX bound to all the species-C adenoviruses examined, no densities were seen for PF4, even though PF4 can co-pellet with various Ads. Similar to FX, the γ-carboxyglutamic acid (Gla) domain of FII binds within the surface cavity of hexon trimers. While FII binds equally to species-C Ads: Ad5, Ad6, and Ad657, FX exhibits significantly better binding to Ad5 and Ad657 compared to Ad6. Although only the FX-Gla domain is observed at high-resolution (3.7 Å), the entire FX is visible at low-resolution bound to Ad5 in three equivalent binding modes consistent with the 3-fold symmetric hexon. Only the Gla and kringle-1 domains of FII are visible on all the species-C adenoviruses, where the rigid FII binds in an upright fashion, in contrast to the flexible and bent FX. These data suggest that differential binding of FII and FX may shield certain species-C adenoviruses differently against immune molecules, thereby modulating their tropism.


  • Organizational Affiliation

    Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic, Rochester, MN, 55905, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hexon proteinA [auth J],
B [auth K],
C [auth L]
952Human adenovirus 5Mutation(s): 0 
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5)
Explore P04133 
Go to UniProtKB:  P04133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04133
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XD [auth Z]488Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI161367

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release