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- EMDB-75027: Adenovirus comprising hexons displaying BAP in the HVR5 region -

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Basic information

Entry
Database: EMDB / ID: EMD-75027
TitleAdenovirus comprising hexons displaying BAP in the HVR5 region
Map data
Sample
  • Complex: Modified human adenovirus 6
KeywordsViral vectors / Capsid engineering / Zwitterionic peptides / Qdenoviruses / Immune stealth / Blood factors / Neutralizing antibodies / Cryo-EM / VIRUS
Biological speciesModified human adenovirus 6
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsReddy VS / Ma OS
Funding support2 items
OrganizationGrant numberCountry
Not funded
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 8, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75027.png

Downloads & links

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Map

FileDownload / File: emd_75027.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 800 pix.
= 1126.4 Å		1.41 Å/pix.
x 800 pix.
= 1126.4 Å		1.41 Å/pix.
x 800 pix.
= 1126.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.28037232 - 0.86780506
Average (Standard dev.)0.018751217 (±0.08096351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1126.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75027_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_75027_half_map_2.map
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Sample components

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Entire : Modified human adenovirus 6

EntireName: Modified human adenovirus 6
Components
  • Complex: Modified human adenovirus 6

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Supramolecule #1: Modified human adenovirus 6

SupramoleculeName: Modified human adenovirus 6 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Modified human adenovirus 6
Molecular weightTheoretical: 150 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.2 / Component - Concentration: 20.0 mM / Component - Name: HEPES / Details: 300mM NaCl, 20mM HEPES pH 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 3 / Number real images: 6515 / Average exposure time: 20.0 sec. / Average electron dose: 51.0 e/Å2 / Details: Movie mode 40 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 86317
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Human adenovirus 6 map available in the lab
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 74007
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation

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