13EU | pdb_000013eu

Cryo-EM structure of HAdV-C6 hexon trimer in complex with human coagulation factor X (FX)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 13EU

This is version 1.1 of the entry. See complete history

Literature

Structural requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion.

Ma, O.X.Lu, S.C.Mudrick, H.E.Barry, M.E.French, J.B.Barry, M.A.Reddy, V.S.

(2026) PLoS Pathog 22: e1014389-e1014389

  • DOI: https://doi.org/10.1371/journal.ppat.1014389
  • Primary Citation Related Structures: 
    13CM, 13DJ, 13DM, 13ER, 13ES, 13EU

  • PubMed Abstract: 

    Human adenovirus serotype 5 (HAdV-C5) is widely used as a gene delivery vector in both experimental and clinical settings. Upon intravenous administration, HAdV-C5 exhibits strong liver tropism, largely mediated by interactions between its major capsid protein, hexon (Hx), and coagulation factor X (FX). In contrast, the closely related species C adenovirus 6 (HAdV-C6) also targets the liver but shows reduced dependency on coagulation factors, whereas species D adenovirus 26 (HAdV-D26) does not bind coagulation factors altogether. To define the structural basis of this serotype-specific host factor recognition, we determined high-resolution cryo-electron microscopy structures of isolated hexon trimers from HAdV-C5 and HAdV-C6 in complex with coagulation factors FX and prothrombin (factor II, FII). The resulting atomic models reveal conserved binding interfaces involving the γ-carboxyglutamic acid (Gla) domains of both coagulation factors and the hypervariable regions HVR5 and HVR7 lining the surface cavities of HAdV-C5 and HAdV-C6 hexons. Structures of hexon complexes formed by co-incubation with both FX and FII further reveal serotype-specific binding preferences under physiologically relevant conditions, showing that HAdV-C5 hexon preferentially engages FX, whereas HAdV-C6 hexon favors FII. By contrast, HAdV-D26 hexon does not bind either factor, likely due to an insertion constrained by proline residues in the HVR5 loop that restricts the factor access to the hexon cavity. Together, these findings provide a detailed structural framework for adenovirus-coagulation factor interactions and support the rational engineering of adenovirus vectors with improved targeting and safety profiles.


  • Organizational Affiliation
    • The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America.

Macromolecule Content 

  • Total Structure Weight: 373.75 kDa 
  • Atom Count: 22,261 
  • Modeled Residue Count: 2,779 
  • Deposited Residue Count: 3,308 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hexon protein
A, B, C
963Human adenovirus 6Mutation(s): 0 
Gene Names: HexonL3
UniProt
Find proteins for B2ZWX4 (Human adenovirus C serotype 6)
Explore B2ZWX4 
Go to UniProtKB:  B2ZWX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZWX4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor XD [auth G]419Homo 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
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: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21_5207

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: 2026-07-08
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references