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- EMDB-75090: Structure of an adenovirus hexon with Zwitterionic insertion in HVR5 -

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Basic information

Entry
Database: EMDB / ID: EMD-75090
TitleStructure of an adenovirus hexon with Zwitterionic insertion in HVR5
Map data
Sample
  • Complex: Human adenovirus 57
    • Protein or peptide: Hexon protein
KeywordsViral vectors / capsid engineering / zwitterionic peptides / adenoviruses / immune stealth / blood factors / neutralizing antibodies / cryo-EM / VIRUS / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsReddy VS / Ma OX
Funding support1 items
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, 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_75090.png

Downloads & links

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Map

FileDownload / File: emd_75090.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 160 pix.
= 225.28 Å		1.41 Å/pix.
x 160 pix.
= 225.28 Å		1.41 Å/pix.
x 160 pix.
= 225.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.1030357 - 0.15022048
Average (Standard dev.)0.00006813255 (±0.0074308766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 225.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75090_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75090_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 57

EntireName: Human adenovirus 57
Components
  • Complex: Human adenovirus 57
    • Protein or peptide: Hexon protein

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Supramolecule #1: Human adenovirus 57

SupramoleculeName: Human adenovirus 57 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human adenovirus 57
Molecular weightTheoretical: 150 MDa

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 57
Molecular weightTheoretical: 104.375398 KDa
Recombinant expressionOrganism: Human adenovirus 57
SequenceString: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNSCEWDEDD GKKTHVYAQA PFAGEAINKN G LQIGTNGA ...String:
MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNSCEWDEDD GKKTHVYAQA PFAGEAINKN G LQIGTNGA ATEGNKEIYA DKTYQPEPQI GESQWNEAES SVAGGRVLKK TTPMKPCYGS YARPTNSNGG QGVMVEQNGK LE SQVEMQF FSTSSGGTPK LVLYSEDVNM ETPDTHLSYK PGKSDDNSKA MLGQQSMPNR PNYIAFRDNF IGLMYYNSTG NMG VLAGQA SQLNAVVDLQ DRNTELSYQL LLDSIGDRTR YFSMWNQAVD SYDPDVRIIE NHGTEDELPN YCFPLGGIGV TDTY QAIKA TNGNGGATTW AQDNTFAERN EIGVGNNFAM EINLNANLWR NFLYSNIALY LPDKLKYNPT NVEISDNPNT YDYMN KRVV APGLVDCYIN LGARWSLDYM DNVNPFNHHR NAGLRYRSML LGNGRYVPFH IQVPQKFFAI KNLLLLPGSY TYEWNF RKD VNMVLQSSLG NDLRVDGASI KFDSICLYAT FFPMAHNTAS TLEAMLRNDT NDQSFNDYLS AANMLYPIPA NATNVPI SI PSRNWAAFRG WAFTRLKTKE TPSLGSGYDP YYTYSGSIPY LDGTFYLNHT FKKVAITFDS SVSWPGNDRL LTPNEFEI K RSVDGEGYNV AQCNMTKDWF LVQMLANYNI GYQGFYIPES YKDRMYSFFR NFQPMSRQVV DDTKYKDYQQ VGIIHQHNN SGFVGYLAPT MREGQAYPAN VPYPLIGKTA VDSITQKKFL CDRTLWRIPF SSNFMSMGAL TDLGQNLLYA NSAHALDMTF EVDPMDEPT LLYVLFEVFD VVRVHQPHRG VIETVYLRTP FSAGNAT

UniProtKB: Hexon protein

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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 mg/mL
BufferpH: 7.2 / Component - Concentration: 20.0 mM / Component - Name: HEPES / Details: 20mM HEPES pH 7.2 300 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 75.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 3 / Number real images: 6168 / Average exposure time: 20.0 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 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: 55238
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ad6 map available in the lab
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 1780537
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

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

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

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