[English] 日本語
Yorodumi
- EMDB-55342: C1 CHIMPSELS_S57C ADDomer map. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55342
TitleC1 CHIMPSELS_S57C ADDomer map.
Map dataCryo-EM map of the full CHIMPSELS_S57C ADDomer without symmetry applied.
Sample
  • Complex: CHIMPSELS S57C ADDomer: An engineered viral like particle derived from penton base protein of Chimpanzee adenovirus Y25.
KeywordsAdenovirus / Nanoparticle / Disulphide bond / Thermostable. / VIRUS LIKE PARTICLE
Biological speciesChimpanzee adenovirus Y25
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBalchin G / Berger-Schaffitzel C / Berger I
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Engineering and Physical Sciences Research Council United Kingdom
European Research Council (ERC)European Union
CitationJournal: ACS Synth Biol / Year: 2026
Title: Engineering the ADDomer Nanoparticle Vaccine Scaffold for Improved Assembly and Enhanced Stability.
Authors: Georgia Balchin / Burak V Kabasakal / Alessandro Strofaldi / Sophie Hall / Charlotte Fletcher / Dora Buzas / Joshua C Bufton / Sathish K N Yadav / Dakang Shen / Frederic Garzoni / H Adrian ...Authors: Georgia Balchin / Burak V Kabasakal / Alessandro Strofaldi / Sophie Hall / Charlotte Fletcher / Dora Buzas / Joshua C Bufton / Sathish K N Yadav / Dakang Shen / Frederic Garzoni / H Adrian Bunzel / Jennifer J McManus / Christiane Schaffitzel / Imre Berger /
Abstract: Virus-like particles (VLPs) are promising platforms for next-generation vaccines due to their ability to present antigens in highly ordered, repetitive geometries emulating pathogen-associated ...Virus-like particles (VLPs) are promising platforms for next-generation vaccines due to their ability to present antigens in highly ordered, repetitive geometries emulating pathogen-associated patterns to elicit potent immune responses. The ADDomer is a synthetic dodecahedral VLP scaffold derived from the penton base protein (PBP) of human adenovirus serotype 3 (Ad3). PBP tolerates insertion of multiple antigenic epitopes in flexible surface-exposed loops, and spontaneously self-assembles into ADDomer nanoparticles, but faces limitations including incomplete assembly and susceptibility to preexisting antihuman adenovirus immunity. Here, we report two complementary engineering strategies to enhance ADDomer robustness. First, we developed a Chimpanzee adenovirus Y25-based ADDomer (CHIMPSELS) to circumvent preexisting antihuman adenovirus immunity, and introduced a point mutation to restore a motif critical for dodecahedron integrity. Second, we introduced targeted intersubunit disulfide bonds to reinforce particle assembly. High-resolution electron cryo-microscopy confirmed the formation of intact dodecahedral particles, revealing that disulfide bonds stabilize distinct conformations of the PBP N-termini. Differential scanning fluorimetry and dynamic light scattering demonstrated thermal stability and elevated aggregation onset temperatures in the disulfide-stabilized ADDomers, providing a scalable assay for screening ADDomer-based VLP constructs for vaccine development. Incorporation of validated immunogenic epitopes, including a SARS-CoV-2 receptor-binding motif segment and the Chikungunya E2EP3 peptide, demonstrated structural integrity and epitope display by the modified scaffolds. Our results establish a versatile, thermostable VLP platform with reduced susceptibility to preexisting immunity, improved particle integrity, and capacity for modular epitope presentation. This work advances the ADDomer toward practical applications in vaccine development and highlights engineering strategies that can be broadly applied to enhance the performance of protein-based VLP vaccines.
History
DepositionOct 10, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55342.png

Downloads & links

-
Map

FileDownload / File: emd_55342.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the full CHIMPSELS_S57C ADDomer without symmetry applied.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 392 pix.
= 419.44 Å		1.07 Å/pix.
x 392 pix.
= 419.44 Å		1.07 Å/pix.
x 392 pix.
= 419.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.05720363 - 0.107498765
Average (Standard dev.)0.00012194132 (±0.0069362666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 419.44003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55342_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of the full CHIMPSELS S57C ADDomer...

Fileemd_55342_half_map_1.map
AnnotationHalf map 2 of the full CHIMPSELS_S57C ADDomer without symmetry applied.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of the full CHIMPSELS S57C ADDomer...

Fileemd_55342_half_map_2.map
AnnotationHalf map 1 of the full CHIMPSELS_S57C ADDomer without symmetry applied.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CHIMPSELS S57C ADDomer: An engineered viral like particle derived...

EntireName: CHIMPSELS S57C ADDomer: An engineered viral like particle derived from penton base protein of Chimpanzee adenovirus Y25.
Components
  • Complex: CHIMPSELS S57C ADDomer: An engineered viral like particle derived from penton base protein of Chimpanzee adenovirus Y25.

-
Supramolecule #1: CHIMPSELS S57C ADDomer: An engineered viral like particle derived...

SupramoleculeName: CHIMPSELS S57C ADDomer: An engineered viral like particle derived from penton base protein of Chimpanzee adenovirus Y25.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: ADDomer produced by recombinant expression of the engineered penton base protein of Chimpanzee adenovirus Y25 using the MultiBac baculovirus-insect cell expression system. 60 penton base ...Details: ADDomer produced by recombinant expression of the engineered penton base protein of Chimpanzee adenovirus Y25 using the MultiBac baculovirus-insect cell expression system. 60 penton base proteins self assemble into the ADDomer particle.
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 3.65 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClsodium chloride
0.2 mMEDTAEthylenediaminetetraacetic acid
0.1 mMAEBSF4-(2-Aminoethyl)benzenesulfonyl fluoride
100.0 uMDichloro(1,10-phenanthroline)copper(II)Copper Phenanthroline
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16511 / Average exposure time: 3.846 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2464479
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: used a 60 angstrom low pass filtered map of the CHIMPSELS ADDomer.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 245875
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: The CHIMPSELS ADDomer model was used an initial model source.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more