9YD0 | pdb_00009yd0

Structure of the Adenovirus-7 VLP, Class 1

  • Classification: VIRUS LIKE PARTICLE
  • Organism(s): Human adenovirus 7
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-09-20 Released: 2026-07-01 
  • Deposition Author(s): Khayat, R., Madoo, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation, Department of Defense (DOD, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structure of Human adenovirus 7 virus-like particles, a platform for developing nanotherapeutics and studying capsid assembly.

Madoo, K.Mazboudi, R.Islam, Z.M.Luo, J.Kuschner, R.A.Gottlieb, P.Dennehy, J.J.Abzalimov, R.R.Galarza, J.M.Khayat, R.

(2026) Proc Natl Acad Sci U S A 123: e2526969123-e2526969123

  • DOI: https://doi.org/10.1073/pnas.2526969123
  • Primary Citation Related Structures: 
    9YCH, 9YCI, 9YCJ, 9YD0

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The City College of New York at The City University of New York, New York, NY 10031.

Macromolecule Content 

  • Total Structure Weight: 1,655.22 kDa 
  • Atom Count: 95,138 
  • Modeled Residue Count: 12,046 
  • Deposited Residue Count: 14,838 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-protein VI250Human adenovirus 7Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for Q5EY64 (Human adenovirus B serotype 7)
Explore Q5EY64 
Go to UniProtKB:  Q5EY64
Entity Groups
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UniProt GroupQ5EY64
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hexon protein937Human adenovirus 7Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P36851 (Human adenovirus B serotype 7)
Explore P36851 
Go to UniProtKB:  P36851
Entity Groups
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UniProt GroupP36851
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-hexon-linking protein IIIaR [auth M]588Human adenovirus 7Mutation(s): 0 
Gene Names: L1
UniProt
Find proteins for Q5EY68 (Human adenovirus B serotype 7)
Explore Q5EY68 
Go to UniProtKB:  Q5EY68
Entity Groups
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UniProt GroupQ5EY68
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Hexon-interlacing protein IXS [auth P],
T [auth Q],
U [auth R],
V [auth S]
138Human adenovirus 7Mutation(s): 0 
Gene Names: IX
UniProt
Find proteins for P68971 (Human adenovirus B serotype 7)
Explore P68971 
Go to UniProtKB:  P68971
Entity Groups
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UniProt GroupP68971
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-hexon-linking protein VIIIW [auth U],
X [auth V]
227Human adenovirus 7Mutation(s): 0 
Gene Names: L4
UniProt
Find proteins for Q5EY56 (Human adenovirus B serotype 7)
Explore Q5EY56 
Go to UniProtKB:  Q5EY56
Entity Groups
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UniProt GroupQ5EY56
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.19

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5SC1GM139701
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5G12MD007603-30
Simons FoundationUnited States349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Department of Defense (DOD, United States)United StatesW81XH19C0169

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release