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- EMDB-72794: Structure of the Adenovirus-7 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-72794
TitleStructure of the Adenovirus-7 VLP
Map data
Sample
  • Virus: Human adenovirus 7
KeywordsAdenovirus / vaccine / VLP / maturation / VIRUS LIKE PARTICLE
Biological speciesHuman adenovirus 7
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKhayat R / Madoo K
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5SC1GM139701 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5G12MD007603-30 United States
Simons Foundation349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Department of Defense (DOD, United States)W81XH19C0169 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structure of Human adenovirus 7 virus-like particles, a platform for developing nanotherapeutics and studying capsid assembly.
Authors: Kiyano Madoo / Ryan Mazboudi / Zubaida Marufee Islam / Jonathan Luo / Robert A Kuschner / Paul Gottlieb / John J Dennehy / Rinat R Abzalimov / Jose M Galarza / Reza Khayat /
Abstract: Adenoviridae family members routinely infect humans, exhibit significant genetic diversity, and are associated with a variety of illnesses. Types 4 and 7 frequently circulate in the United States and ...Adenoviridae family members routinely infect humans, exhibit significant genetic diversity, and are associated with a variety of illnesses. Types 4 and 7 frequently circulate in the United States and are major causes of respiratory disease. Infections can result in hospitalization and, in severe cases, death. Although a live wild-type-virus vaccine targeting these two types exists, its use is restricted to military personnel due to concerns about viral-shedding and potential for genetic recombination. To overcome these limitations, we recently developed a virus-like particle (VLP) platform as an alternative vaccination strategy. These VLPs are stable, lack genomic material, and elicit a potent humoral immune response in mice, effectively neutralizing adenoviral infection. Here, we describe the cryo-EM structure of adenovirus 7 (AdV-7) VLPs. Structural insights are essential to ensure that neutralizing antigens displayed on the VLPs accurately mimic those of the virion, guide the design of particles with improved stability and efficacy, and enable engineering of VLPs with antigenic properties targeting multiple adenovirus types. The structure shows that hexon, penton, pIIIa, pVI, pVIII, and IX assemble comparable to AdV-5, hexon and penton neutralizing epitopes are appropriately displayed for antibody recognition, penton insertion into the hexon shell promotes cement protein pIIIa to increase its interaction with the peripentonal hexons, and presence of the core-genome is associated with increased interaction between cement protein pVIII and hexon. Finally, limited proteolysis and mass spectrometry demonstrate that VLP incorporated hexons digest more readily than virion incorporated hexons, indicating the greater dynamic nature of the VLP.
History
DepositionSep 21, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72794.png

Downloads & links

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Map

FileDownload / File: emd_72794.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 1280 pix.
= 1386.24 Å		1.08 Å/pix.
x 1280 pix.
= 1386.24 Å		1.08 Å/pix.
x 1280 pix.
= 1386.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.052835 - 11.442728000000001
Average (Standard dev.)-0.000000000063739 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1386.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72794_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72794_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 7

EntireName: Human adenovirus 7
Components
  • Virus: Human adenovirus 7

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Supramolecule #1: Human adenovirus 7

SupramoleculeName: Human adenovirus 7 / type: virus / ID: 1 / Parent: 0 / Details: Adenovirus 7 Virus-like particles / NCBI-ID: 10519 / Sci species name: Human adenovirus 7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.2 MDa
Virus shellShell ID: 1 / Name: Hexon / Diameter: 960.0 Å / T number (triangulation number): 25

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 13608 / Average exposure time: 50.0 sec. / Average electron dose: 53.35 e/Å2 / Details: Not all images had particles
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 2.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 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. 4.13) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.03) / Number images used: 15808
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.13)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.13)

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