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- EMDB-0198: Synthetic Self-assembling ADDomer Platform for Highly Efficient V... -

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Basic information

Entry
Database: EMDB / ID: EMD-0198
TitleSynthetic Self-assembling ADDomer Platform for Highly Efficient Vaccination by Genetically-encoded Multi-epitope Display
Map dataADDomer dodecahedron (engineered viral like particle derived from Ad3 Penton base protein). RELION Post Processed (Masked and B-factor sharpened map).
Sample
  • Complex: ADDomer: An engineered viral like particle derived from penton base protein of Human adenovirus B3 (Ad3).
    • Protein or peptide: Penton protein
Keywordsengineered / virus / like / particle / ADDomer / Ad3 / penton / base / adenovirus / synthetic / vaccine / biobrick / human / homosapien / dodecahedron / icosohedral / epitode / display / scaffold / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding / Penton protein
Function and homology information
Biological speciesHuman adenovirus B3 / Human adenovirus B serotype 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBufton JC / Berger I
CitationJournal: Sci Adv / Year: 2019
Title: Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display.
Authors: Charles Vragniau / Joshua C Bufton / Frédéric Garzoni / Emilie Stermann / Fruzsina Rabi / Céline Terrat / Mélanie Guidetti / Véronique Josserand / Matt Williams / Christopher J Woods / ...Authors: Charles Vragniau / Joshua C Bufton / Frédéric Garzoni / Emilie Stermann / Fruzsina Rabi / Céline Terrat / Mélanie Guidetti / Véronique Josserand / Matt Williams / Christopher J Woods / Gerardo Viedma / Phil Bates / Bernard Verrier / Laurence Chaperot / Christiane Schaffitzel / Imre Berger / Pascal Fender /
Abstract: Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein- ...Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein-based self-assembling nanoparticle scaffold engineered to facilitate plug-and-play display of multiple immunogenic epitopes from pathogens. We used cryo-electron microscopy at near-atomic resolution and implemented novel, cost-effective, high-performance cloud computing to reveal architectural features in unprecedented detail. We analyzed ADDomer interaction with components of the immune system and developed a promising first-in-kind ADDomer-based vaccine candidate to combat emerging Chikungunya infectious disease, exemplifying the potential of our approach.
History
DepositionAug 16, 2018-
Header (metadata) releaseSep 26, 2018-
Map releaseAug 28, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hcr
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hcr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0198.png

Downloads & links

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Map

FileDownload / File: emd_0198.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationADDomer dodecahedron (engineered viral like particle derived from Ad3 Penton base protein). RELION Post Processed (Masked and B-factor sharpened map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375 / Movie #1: 0.0375
Minimum - Maximum-0.10433917 - 0.18376105
Average (Standard dev.)0.0007156278 (±0.0073639005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1040.1840.001

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Supplemental data

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Sample components

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Entire : ADDomer: An engineered viral like particle derived from penton ba...

EntireName: ADDomer: An engineered viral like particle derived from penton base protein of Human adenovirus B3 (Ad3).
Components
  • Complex: ADDomer: An engineered viral like particle derived from penton base protein of Human adenovirus B3 (Ad3).
    • Protein or peptide: Penton protein

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Supramolecule #1: ADDomer: An engineered viral like particle derived from penton ba...

SupramoleculeName: ADDomer: An engineered viral like particle derived from penton base protein of Human adenovirus B3 (Ad3).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed and purified ADDomer complex (penton base dodecahedron).
Source (natural)Organism: Human adenovirus B3
Molecular weightTheoretical: 3.811834 MDa

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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 B serotype 3
Molecular weightTheoretical: 63.598293 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRRRAVLGGA VVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGEFV T VNDGPVND ...String:
MRRRAVLGGA VVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGEFV T VNDGPVND TYDHKEDILK YEWFEFILPE GNFSATMTID LMNNAIIDNY LEIGRQNGVL ESDIGVKFDT RNFRLGWDPE TK LIMPGVY TYEAFHPDIV LLPGCGVDFT ESRLSNLLGI RKRHPFQEGF KIMYEDLEGG NIPALLDVTA YEESKKDTTT ARE TTTLAV AEETSEDVDD DITRGDTYIT ELEKQKREAA AAEVSRKKEL KIQPLEKDSK SRSYNVLEDK INTAYRSWYL SYNY GNPEK GIRSWTLLTT SDVTCGAEQV YWSLPDMMQD PVTFRSTRQV NNYPVVGAEL MPVFSKSFYN EQAVYSQQLR QATSL THVF NRFPENQILI RPPAPTITTV SENVPALTDH GTLPLRSSIR GVQRVTVTDA RRRTCPYVYK ALGIVAPRVL SSRTF

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
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1060 / Average exposure time: 0.25 sec. / Average electron dose: 1.3125 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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:

4ar2

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 1758
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4ar2


Chain - Chain ID: A / Chain - Residue range: 61-542 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe model was adjusted to fit into the map manually using COOT before further iterative positional and B-factor refinement in real space using Phenix Real-Space refinement software. Final adjustments were carried out in COOT.
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6hcr:
Synthetic Self-assembling ADDomer Platform for Highly Efficient Vaccination by Genetically-encoded Multi-epitope Display

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