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- PDB-3izo: Model of the fiber tail and its interactions with the penton base... -

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Basic information

Entry
Database: PDB / ID: 3izo
TitleModel of the fiber tail and its interactions with the penton base of human adenovirus by cryo-electron microscopy
Components
  • Fiber
  • Penton protein
KeywordsVIRAL PROTEIN / human adenovirus fiber tail / pentameric penton base / trimeric fiber
Function / homology
Function and homology information


T=25 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral capsid / clathrin-dependent endocytosis of virus by host cell / cell adhesion / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / nucleus
Similarity search - Function
Penton protein; domain 1 / adenovirus 2 penton base, domain 2 / adenovirus 2 penton base, domain 2 / Adenovirus penton base protein / Adenovirus penton base protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein ...Penton protein; domain 1 / adenovirus 2 penton base, domain 2 / adenovirus 2 penton base, domain 2 / Adenovirus penton base protein / Adenovirus penton base protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Jelly Rolls / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penton protein / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, H.
CitationJournal: J Mol Biol / Year: 2011
Title: Model of the trimeric fiber and its interactions with the pentameric penton base of human adenovirus by cryo-electron microscopy.
Authors: Hongrong Liu / Lily Wu / Z Hong Zhou /
Abstract: Adenovirus invades host cells by first binding to host receptors through a trimeric fiber, which contains three domains: a receptor-binding knob domain, a long flexible shaft domain, and a penton ...Adenovirus invades host cells by first binding to host receptors through a trimeric fiber, which contains three domains: a receptor-binding knob domain, a long flexible shaft domain, and a penton base-attachment tail domain. Although the structure of the knob domain associated with a portion of the shaft has been solved by X-ray crystallography, the in situ structure of the fiber in the virion is not known; thus, it remains a mystery how the trimeric fiber attaches to its underlying pentameric penton base. By high-resolution cryo-electron microscopy, we have determined the structure of the human adenovirus type 5 (Ad5) to 3.6-Å resolution and have reported the full atomic models for its capsid proteins, but not for the fiber whose density cannot be directly interpreted due to symmetry mismatch with the penton base. Here, we report the determination of the Ad5 fiber structure and its mode of attachment to the pentameric penton base by using an integrative approach of multi-resolution filtering, homology modeling, computational simulation of mismatched symmetries, and fitting of atomic models into cryo-electron microscopy density maps. Our structure reveals that the interactions between the trimeric fiber and the pentameric penton base are mediated by a hydrophobic ring on the top surface of the penton base and three flexible tails inserted into three of the five available grooves formed by neighboring subunits of penton base. These interaction sites provide the molecular basis for the symmetry mismatch and can be targeted for optimizing adenovirus for gene therapy applications.
History
DepositionNov 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Apr 5, 2023Group: Database references / Category: database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_id / _pdbx_database_related.details

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Structure visualization

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Assembly

Deposited unit
A: Penton protein
F: Fiber
B: Penton protein
G: Fiber
C: Penton protein
D: Penton protein
H: Fiber
E: Penton protein


Theoretical massNumber of molelcules
Total (without water)501,6828
Polymers501,6828
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Penton protein / / Penton base protein / Virion component III / pIII


Mass: 63356.602 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 5 / Strain: HEK 293 cell / References: UniProt: P12538
#2: Protein Fiber /


Mass: 61633.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 5 / Strain: HEK 293 cell / References: UniProt: Q7T416

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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: Human adenovirus type 5 / Type: VIRUS
Buffer solutionpH: 7.5 / Details: 10mM Tris-HCL,1mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: IMIRS / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common lines for orientation and center refinement icosahedral symmetry-adapted functions for 3D reconstruction
Resolution: 3.6 Å / Num. of particles: 31815 / Nominal pixel size: 1.076 Å / Actual pixel size: 1.1 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms18537 0 0 0 18537

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