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- EMDB-75053: Adenovirus hexon displaying BAP insertion in the HVR5 region -

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Basic information

Entry
Database: EMDB / ID: EMD-75053
TitleAdenovirus hexon displaying BAP insertion in the HVR5 region
Map dataLocalized reconstruction of hexon-4 of Ad657_BAP at 3.2A resolution.
Sample
  • Complex: Human adenovirus 57
    • Protein or peptide: BAP inserted Hexon protein
KeywordsViral vectors / capsid engineering / zwitterionic peptides / adenoviruses / immune stealth / blood factors / neutralizing antibodies / cryo-EM / VIRUS / VIRAL PROTEIN
Biological speciesHuman adenovirus 57 / Human adenovirus 6
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 10, 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_75053.png

Downloads & links

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Map

FileDownload / File: emd_75053.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstruction of hexon-4 of Ad657_BAP at 3.2A resolution.
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: 0.003
Minimum - Maximum-0.035846926 - 0.050360758
Average (Standard dev.)0.00014932368 (±0.0024389974)
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_75053_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_75053_half_map_2.map
Projections & Slices
AxesZYX

Projections

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: BAP inserted 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

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Macromolecule #1: BAP inserted Hexon protein

MacromoleculeName: BAP inserted Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 6
Molecular weightTheoretical: 111.164336 KDa
Recombinant expressionOrganism: Human adenovirus 6
SequenceString: MMPQWSYMHI SGQDASEYLS PGLVQFARAT ETYFSLNNKF RNPTVAPTHD VTTDRSQRLT LRFIPVDRED TAYSYKARFT LAVGDNRVL DMASTYFDIR GVLDRGPTFK PYSGTAYNAL APKGAPNSCE WDEDDGKKTH VYAQAPFAGE AINKNGLQIG T NGAATEGN ...String:
MMPQWSYMHI SGQDASEYLS PGLVQFARAT ETYFSLNNKF RNPTVAPTHD VTTDRSQRLT LRFIPVDRED TAYSYKARFT LAVGDNRVL DMASTYFDIR GVLDRGPTFK PYSGTAYNAL APKGAPNSCE WDEDDGKKTH VYAQAPFAGE AINKNGLQIG T NGAATEGN KEIYADKTYQ PEPQIGESQW NEAESSVAGG RVLKKTTPMK PCYGSYARPT NSNGGQGVMV EQNGKLESQV EM QFFSTST GEIPAPLAGT VSKILVKEGD TVKAGQTVLV LEAMKMETEI NAPTDGKVEK VLVKERDAVQ GGQGLIKIGG GTP KLVLYS EDVNMETPDT HLSYKPGKSD DNSKAMLGQQ SMPNRPNYIA FRDNFIGLMY YNSTGNMGVL AGQASQLNAV VDLQ DRNTE LSYQLLLDSI GDRTRYFSMW NQAVDSYDPD VRIIENHGTE DELPNYCFPL GGIGVTDTYQ AIKATNGNGG ATTWA QDNT FAERNEIGVG NNFAMEINLN ANLWRNFLYS NIALYLPDKL KYNPTNVEIS DNPNTYDYMN KRVVAPGLVD CYINLG ARW SLDYMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHIQVPQ KFFAIKNLLL LPGSYTYEWN FRKDVNMVLQ SSLGNDL RV DGASIKFDSI CLYATFFPMA HNTASTLEAM LRNDTNDQSF NDYLSAANML YPIPANATNV PISIPSRNWA AFRGWAFT R LKTKETPSLG SGYDPYYTYS GSIPYLDGTF YLNHTFKKVA ITFDSSVSWP GNDRLLTPNE FEIKRSVDGE GYNVAQCNM TKDWFLVQML ANYNIGYQGF YIPESYKDRM YSFFRNFQPM SRQVVDDTKY KDYQQVGIIH QHNNSGFVGY LAPTMREGQA YPANVPYPL IGKTAVDSIT QKKFLCDRTL WRIPFSSNFM SMGALTDLGQ NLLYANSAHA LDMTFEVDPM DEPTLLYVLF E VFDVVRVH QPHRGVIETV YLRTPFSAGN ATT

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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 7.2, 300mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus min: 1.6 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

CTF correctionSoftware - Name: cryoSPARC (ver. 3.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ad6 hexon
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 4440390
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
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
Output model

PDB-10bu:
Adenovirus hexon displaying BAP insertion in the HVR5 region

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