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- PDB-13eu: Cryo-EM structure of HAdV-C6 hexon trimer in complex with human c... -

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Basic information

Entry
Database: PDB / ID: 13eu
TitleCryo-EM structure of HAdV-C6 hexon trimer in complex with human coagulation factor X (FX)
Components
  • Coagulation factor X
  • Hexon protein
KeywordsVIRAL PROTEIN / adenovirus / hexon / coagulation factor X / virus-host interaction / cryo-EM / virus capsid
Function / homology
Function and homology information


T=25 icosahedral viral capsid / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / : / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : ...T=25 icosahedral viral capsid / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / : / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / : / phospholipid binding / Golgi lumen / blood coagulation / host cell / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / external side of plasma membrane / calcium ion binding / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / : / extracellular region / plasma membrane
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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily ...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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Calcium-binding EGF-like domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Hexon protein / Coagulation factor X
Similarity search - Component
Biological speciesHuman adenovirus 6
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 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
DepositionMay 3, 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
G: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,74711
Polymers373,4664
Non-polymers2817
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: 108635.133 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The modeled structure lacks the N-terminal residues 1-6, an internal region corresponding to residues 139-164, and a short segment around residues 445-452, as well as the C-terminal residues ...Details: The modeled structure lacks the N-terminal residues 1-6, an internal region corresponding to residues 139-164, and a short segment around residues 445-452, as well as the C-terminal residues 948-952. These regions were not included in the model due to the absence of well-defined cryo-EM density.
Source: (gene. exp.) Human adenovirus 6 / Gene: Hexon, L3 / Production host: Human adenovirus 6 / References: UniProt: B2ZWX4
#2: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 47560.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The modeled coagulation factor X (FX) corresponds to the N-terminal Gla domain, while the signal peptide, propeptide, and the remainder of the protein (including EGF-like domains and the ...Details: The modeled coagulation factor X (FX) corresponds to the N-terminal Gla domain, while the signal peptide, propeptide, and the remainder of the protein (including EGF-like domains and the protease domain) are not included in the model due to absence of interpretable cryo-EM density. The retained region contains multiple gamma-carboxyglutamic acid (Gla) residues required for calcium coordination.
Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P00742, coagulation factor Xa
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 6 hexon trimer in complex with FX
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.39 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 6
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: 3510
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Coot0.9.8.92ELmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 280503
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68552 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222829
ELECTRON MICROSCOPYf_angle_d0.46731042
ELECTRON MICROSCOPYf_dihedral_angle_d13.6168321
ELECTRON MICROSCOPYf_chiral_restr0.0423291
ELECTRON MICROSCOPYf_plane_restr0.0044090

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