+Open data
-Basic information
Entry | Database: PDB / ID: 8qbx | ||||||
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Title | Chimeric Adenovirus-derived dodecamer | ||||||
Components | Penton protein | ||||||
Keywords | VIRUS LIKE PARTICLE / Adenovirus / capsid protein / virus-like particle | ||||||
Function / homology | Adenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding / Penton protein Function and homology information | ||||||
Biological species | Human adenovirus sp. | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Buzas, D. / Borucu, U. / Bufton, J. / Kapadalakere, S.Y. / Toelzer, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2024 Title: Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders. Authors: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre ...Authors: Dora Buzas / Huan Sun / Christine Toelzer / Sathish K N Yadav / Ufuk Borucu / Gunjan Gautam / Kapil Gupta / Joshua C Bufton / Julien Capin / Richard B Sessions / Frederic Garzoni / Imre Berger / Christiane Schaffitzel / Abstract: Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based ...Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based therapeutics independent of a cold chain. To expand the scope of ADDomers for new applications, we engineered ADDobodies, representing PBP crown domain, genetically separated from PBP multimerization domain. We inserted heterologous sequences into hyper-variable loops, resulting in monomeric, thermostable ADDobodies expressed at high yields in Escherichia coli. The X-ray structure of an ADDobody prototype validated our design. ADDobodies can be used in ribosome display experiments to select a specific binder against a target, with an enrichment factor of ∼10-fold per round. ADDobodies can be re-converted into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 Å electron cryo-microscopy structure. Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qbx.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8qbx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qbx_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8qbx_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8qbx_validation.xml.gz | 495.9 KB | Display | |
Data in CIF | 8qbx_validation.cif.gz | 803 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/8qbx ftp://data.pdbj.org/pub/pdb/validation_reports/qb/8qbx | HTTPS FTP |
-Related structure data
Related structure data | 18323MC 8coiC 8qb3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 63195.812 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus sp. / Gene: L2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2Y0H9 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: unidentified adenovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: unidentified adenovirus |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 1.06 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.18.2_3874: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 566795 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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