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- PDB-13dj: HAdV-C5 hexon trimer -

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Basic information

Entry
Database: PDB / ID: 13dj
TitleHAdV-C5 hexon trimer
ComponentsHexon protein
KeywordsVIRAL PROTEIN / adenovirus / hexon / cryo-EM / virus capsid
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMa, O.X. / Reddy, V.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion.
Authors: Olivia X Ma / Shao-Chia Lu / Haley E Mudrick / Mary E Barry / Jarrod B French / Michael A Barry / Vijay S Reddy /
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, ...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.
History
DepositionApr 30, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein


Theoretical massNumber of molelcules
Total (without water)324,3233
Polymers324,3233
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hexon protein / CP-H / Protein II


Mass: 108107.617 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 5 / References: UniProt: P04133
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Purified Human adenovirus type 5 hexon trimer / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.33 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 5
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 6664
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 9759324
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172028 / Symmetry type: POINT
RefinementHighest resolution: 3.17 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00122599
ELECTRON MICROSCOPYf_angle_d0.40730732
ELECTRON MICROSCOPYf_dihedral_angle_d8.8448283
ELECTRON MICROSCOPYf_chiral_restr0.0423246
ELECTRON MICROSCOPYf_plane_restr0.0044047

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