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- PDB-9ycj: Structure of the Adenovirus-7 VLP, Class 2 -

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Basic information

Entry
Database: PDB / ID: 9ycj
TitleStructure of the Adenovirus-7 VLP, Class 2
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein IX
  • Penton protein
  • Pre-protein VI
KeywordsVIRUS LIKE PARTICLE / Adenovirus / vaccine / VLP
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / viral procapsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / viral procapsid / lysis of host organelle involved in viral entry into host cell / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / 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 / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon protein / Hexon-interlacing protein IX / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-hexon-linking protein IIIa / Penton protein
Similarity search - Component
Biological speciesHuman adenovirus 7
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKhayat, R. / Madoo, K.
Funding support United States, 5items
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.USA / Year: 2026
Title: Structure of Human adenovirus 7 virus-like particles, a platform for developing nanotherapeutics and studying capsid assembly.
Authors: 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.
History
DepositionSep 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Pre-protein VI
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Pre-hexon-linking protein IIIa
N: Penton protein
P: Hexon-interlacing protein IX
Q: Hexon-interlacing protein IX
R: Hexon-interlacing protein IX
S: Hexon-interlacing protein IX
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
Y: Pre-protein VI
Z: Pre-protein VI


Theoretical massNumber of molelcules
Total (without water)1,717,16628
Polymers1,717,16628
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 25 molecules 01234WYZABCDEFGHIJKLNPQRS

#1: Protein
Pre-protein VI / pVI


Mass: 27178.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: Q5EY64
#2: Protein
Hexon protein / CP-H / Protein II


Mass: 105807.125 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: P36851
#4: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 61941.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L2 / Production host: Homo sapiens (human) / References: UniProt: Q9JFT6
#5: Protein
Hexon-interlacing protein IX / Protein IX


Mass: 13125.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Due to the low quality of map in certain regions, the identites of some of the amino acids in the model were left as unknown (UNK).
Source: (gene. exp.) Human adenovirus 7 / Gene: IX / Production host: Homo sapiens (human) / References: UniProt: P68971

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Pre-hexon-linking protein ... , 2 types, 3 molecules MUV

#3: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 65798.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: Q5EY68
#6: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24902.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 7 / Gene: L4 / Production host: Homo sapiens (human) / References: UniProt: Q5EY56

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Details

Has protein modificationN
Sequence detailsMany residues of chains P, Q, R, and S, comprised of entity 5 (Protein IX) were not identified, and ...Many residues of chains P, Q, R, and S, comprised of entity 5 (Protein IX) were not identified, and modeled as UNK. The actual sequence is: MSGSASFEGGVFSPYLTGRLPPWAGVRQNVMGSTVDGRPVQPANSSTLTYATLSSSPLDAAAAAAATAAANTILGMGYYG SIVANSSSSNNPSTLAEDKLLVLLAQLEALTQRLGELSKQVAQLREQTESAVATAKSK

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Adenovirus 7 Virus-like particles / Type: COMPLEX / Details: Adenovirus 7 Virus-like particles / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 18.2 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus 7
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 50 sec. / Electron dose: 53.35 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13608 / Details: Not all images had particles.
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.13particle selectionManual Picking
2Leginonimage acquisition
4cryoSPARC4.13CTF correction
7UCSF Chimera1.19model fittingManually fitted as rigid body
9cryoSPARC4.13initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92863 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model

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