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- PDB-9ivx: CryoEM structure of Adenovirus serotype 3 premature hexon in comp... -

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Basic information

Entry
Database: PDB / ID: 9ivx
TitleCryoEM structure of Adenovirus serotype 3 premature hexon in complex with Adenovirus serotype 2 100K
Components
  • Hexon protein
  • Shutoff protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


viral translational shunt / intracellular transport of viral protein in host cell / T=25 icosahedral viral capsid / symbiont-mediated suppression of host translation initiation / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell nucleus ...viral translational shunt / intracellular transport of viral protein in host cell / T=25 icosahedral viral capsid / symbiont-mediated suppression of host translation initiation / microtubule-dependent intracellular transport of viral material towards nucleus / host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Shutoff protein L4 / Late 100kD protein / Adenovirus Pll, hexon, subdomain 3 / 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
Shutoff protein / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus B3
Human adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.23 Å
AuthorsLiu, Q. / Li, H. / Xiang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of the viral encoded chaperone 100K in capsid folding and assembly of adenovirus.
Authors: Haining Li / Luyuan Shao / Zhe Liu / Qi Liu / Ye Xiang /
Abstract: Adenovirus is an icosahedral, non-enveloped DNA virus that infects humans and other animals. The capsid of adenovirus is mainly assembled by the major capsid protein hexon. Folding and assembly of ...Adenovirus is an icosahedral, non-enveloped DNA virus that infects humans and other animals. The capsid of adenovirus is mainly assembled by the major capsid protein hexon. Folding and assembly of hexon require the viral encoded chaperone 100K, of which the detailed structure and chaperoning mechanism remain unknown. Here, we report the cryoEM structure of 100K in complex with a pre-mature hexon trimer. The structure shows that 100K dimers bind to the bottom double jelly-roll domains of the pre-mature hexon, mainly through a hook-like domain and a loop extruded from the dimerization domain. Additionally, a groove formed at the dimerization interface of 100K accommodates the N-terminal fragment 49-53 of an adjacent hexon protomer. Mutagenesis studies indicate that the interactions at the jelly-roll domain and the N-terminus of hexon are all essential for the proper folding and assembly of hexon. 100K binds and stabilizes the partially folded hexon, preventing premature aggregation of hexon, promoting the folding of the hexon top insertion loops, and facilitating hexon trimerization.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexon protein
G: Shutoff protein
F: Shutoff protein
B: Hexon protein
C: Hexon protein
H: Shutoff protein
D: Shutoff protein
I: Shutoff protein
E: Shutoff protein


Theoretical massNumber of molelcules
Total (without water)899,7479
Polymers899,7479
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

#1: Protein Hexon protein / CP-H / Protein II


Mass: 110205.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B3 / Gene: L3, Hexon / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q2Y0H4
#2: Protein
Shutoff protein / 100 kDa protein / p100K / 100K-chaperone protein / L4-100K / Shutoff protein 100K


Mass: 94854.930 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Gene: L4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P24932
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Adenovirus serotype2 100K dimer and serotype3 hexon trimerCOMPLEX#2, #10RECOMBINANT
2Adenovirus serotype2 100K dimerCOMPLEX#21RECOMBINANT
3Adenovirus serotype3 hexon trimerCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Human adenovirus 210515
33Human adenovirus B345659
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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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 defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232424 / Symmetry type: POINT

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