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- EMDB-18323: Chimeric Adenovirus-derived dodecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-18323
TitleChimeric Adenovirus-derived dodecamer
Map data
Sample
  • Virus: unidentified adenovirus
    • Protein or peptide: Penton protein
KeywordsAdenovirus / capsid protein / virus-like particle / 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 / metal ion binding / Penton protein
Function and homology information
Biological speciesHuman adenovirus sp. / unidentified adenovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsBuzas D / Borucu U / Bufton J / Kapadalakere SY / Toelzer C
Funding support United Kingdom, 1 items
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, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18323.png

Downloads & links

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Map

FileDownload / File: emd_18323.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0232
Minimum - Maximum-0.16850562 - 0.30924708
Average (Standard dev.)0.00087228685 (±0.010918029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18323_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1

Fileemd_18323_half_map_1.map
Annotationhalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_18323_half_map_2.map
Annotationhalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : unidentified adenovirus

EntireName: unidentified adenovirus
Components
  • Virus: unidentified adenovirus
    • Protein or peptide: Penton protein

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Supramolecule #1: unidentified adenovirus

SupramoleculeName: unidentified adenovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10535 / Sci species name: unidentified adenovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus sp.
Molecular weightTheoretical: 63.195812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELSPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEYMFSNKF KARVMVSRKA PEGEFVTVND G PVNDTYDH ...String:
MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELSPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEYMFSNKF KARVMVSRKA PEGEFVTVND G PVNDTYDH KEDILKYEWF EFILPEGNFS ATMTIDLMNN AIIDNYLEIG RQNGVLESDI GVKFDTRNFR LGWDPETKLI MP GVYTYEA FHPDIVLLPG CGVDFTESRL SNLLGIRKRH PFQEGFKIMY EDLEGGNIPA LLDVTAYEES KKDTTTARET TTL AVAEET SEDVDDDITR GDTYITELEK QKREAAAAEV SRKKELKIQP LEKDSKSRSY NVLEDKINTA YRSWYLSYNY GNPE KGIRS WTLLTTSDVT CGVEQVYWSL PDMMQDPVTF RSTRQVSNYP VVGAELMPVF SKSFYNEQAV YSQQLRQATS LTHVF NRFP ENQILIRPPA PTITTVSENV PALTDHGTLP LRSSIRGVQR VTVTDARRRT CPYVYKALGI VAPRVLSSRT F

UniProtKB: Penton protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.06 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hcr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 566795
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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