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- PDB-10dk: Structure of an adenovirus hexon with Zwitterionic insertion in HVR5 -

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Basic information

Entry
Database: PDB / ID: 10dk
TitleStructure of an adenovirus hexon with Zwitterionic insertion in HVR5
ComponentsHexon protein
KeywordsVIRAL PROTEIN / Viral vectors / capsid engineering / zwitterionic peptides / adenoviruses / immune stealth / blood factors / neutralizing antibodies / cryo-EM / VIRUS
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / 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 57
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsReddy, V.S. / Ma, O.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther Adv / Year: 2026
Title: Immune shielding of viral vectors via capsid engineering with genetically encoded zwitterionic peptides.
Authors: Shao-Chia Lu / Olivia X Ma / Alex A Anwar / Dimitrije Ratkov / Janarjan Bhandari / Daniel J Montiel-Garcia / Michael J Hansen / Mary E Barry / Vijay S Reddy / Michael A Barry /
Abstract: Pre-existing neutralizing antibodies (NAbs) and blood proteins can rapidly inactivate therapeutic viral vectors and trigger immune toxicities in patients. To overcome these challenges, we engineered ...Pre-existing neutralizing antibodies (NAbs) and blood proteins can rapidly inactivate therapeutic viral vectors and trigger immune toxicities in patients. To overcome these challenges, we engineered the surfaces of adenovirus (Ad) by incorporating genetically encoded "protective shields" to reduce the recognition by host factors. AlphaFold3 modeling showed that inserting a structured biotin acceptor peptide (BAP) into hypervariable region 5 (HVR5) of the viral capsid protein hexon produced a rigid surface protrusion, whereas inserting a disordered, zwitterionic glutamic acid-lysine (EK) peptide formed a flexible canopy over the hexon. Although inserting EK peptides into the capsid impaired viral entry and intracellular trafficking that led to reduced viral transduction and , this modification decreased binding by coagulation factor X (FX) and complement C3. Importantly, the EK peptide-modified Ad also evaded polyclonal anti-Ad NAbs without the need to change all HVRs. The shielding efficiency of EK peptides was affected by their composition and length. Cryoelectron microscopy (cryo-EM) and neutralization assays further revealed that NAbs primarily target HVR1, a region potentially masked by EK peptides inserted in HVR5. These findings demonstrate an alternative capsid engineering approach using genetically encoded peptides to enhance immune stealth of viral vectors.
History
DepositionJan 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)313,1263
Polymers313,1263
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: 104375.398 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 57 / Gene: L3 / Production host: Human adenovirus 57 / References: UniProt: A0A348FV85
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: Human adenovirus 57 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 150 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 57
Source (recombinant)Organism: Human adenovirus 57
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo
Virus shellName: Adenovirus / Diameter: 1000 nm / Triangulation number (T number): 25
Buffer solutionpH: 7.2 / Details: 20mM HEPES pH 7.2 300 mM NaCl
Buffer componentConc.: 20 mM / Name: HEPES
SpecimenConc.: 2 mg/ml / Embedding 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: 95 % / 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 magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 75 K
Image recordingAverage exposure time: 20 sec. / Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6168

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
2EMAN3.2image acquisition
4cryoSPARC4.2CTF correction
7Coot0.9.8.96 EL (CCP4)model fitting
9PHENIX1.18.2-3874model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARC4.2classification
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 55238
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1780537 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00522540
ELECTRON MICROSCOPYf_angle_d0.57130650
ELECTRON MICROSCOPYf_dihedral_angle_d12.3428205
ELECTRON MICROSCOPYf_chiral_restr0.0473230
ELECTRON MICROSCOPYf_plane_restr0.0054054

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