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- PDB-8qbx: Chimeric Adenovirus-derived dodecamer -

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Basic information

Entry
Database: PDB / ID: 8qbx
TitleChimeric Adenovirus-derived dodecamer
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / Adenovirus / capsid protein / virus-like particle
Function / homologyAdenovirus 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 / Penton protein
Function and homology information
Biological speciesHuman adenovirus sp.
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsBuzas, D. / Borucu, U. / Bufton, J. / Kapadalakere, S.Y. / Toelzer, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: 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
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Penton protein
C: Penton protein
A: Penton protein
B: Penton protein
D: Penton protein
E: Penton protein
G: Penton protein
H: Penton protein
I: Penton protein
J: Penton protein
K: Penton protein
L: Penton protein
M: Penton protein
N: Penton protein
O: Penton protein
P: Penton protein
Q: Penton protein
R: Penton protein
S: Penton protein
T: Penton protein
V: Penton protein
W: Penton protein
X: Penton protein
Y: Penton protein
Z: Penton protein
AA: Penton protein
BA: Penton protein
CA: Penton protein
DA: Penton protein
EA: Penton protein
FA: Penton protein
GA: Penton protein
HA: Penton protein
IA: Penton protein
JA: Penton protein
KA: Penton protein
LA: Penton protein
MA: Penton protein
NA: Penton protein
OA: Penton protein
PA: Penton protein
QA: Penton protein
RA: Penton protein
SA: Penton protein
TA: Penton protein
UA: Penton protein
VA: Penton protein
WA: Penton protein
XA: Penton protein
YA: Penton protein
ZA: Penton protein
AB: Penton protein
BB: Penton protein
CB: Penton protein
DB: Penton protein
EB: Penton protein
FB: Penton protein
GB: Penton protein
HB: Penton protein
IB: Penton protein


Theoretical massNumber of molelcules
Total (without water)3,791,74960
Polymers3,791,74960
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Penton 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

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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: unidentified adenovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: unidentified adenovirus
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1.06 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 566795 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004188280
ELECTRON MICROSCOPYf_angle_d0.738257580
ELECTRON MICROSCOPYf_dihedral_angle_d13.0465160
ELECTRON MICROSCOPYf_chiral_restr0.05329580
ELECTRON MICROSCOPYf_plane_restr0.00433240

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