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- EMDB-23266: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-23266
TitleComputationally designed octahedral antibody nanocage with Fc o42.1+Fc
Map dataComputationally designed octahedral antibody nanocage with Fc o42.1+Fc
Sample
  • Complex: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsDang HV / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Science / Year: 2021
Title: Designed proteins assemble antibodies into modular nanocages.
Authors: Robby Divine / Ha V Dang / George Ueda / Jorge A Fallas / Ivan Vulovic / William Sheffler / Shally Saini / Yan Ting Zhao / Infencia Xavier Raj / Peter A Morawski / Madeleine F Jennewein / ...Authors: Robby Divine / Ha V Dang / George Ueda / Jorge A Fallas / Ivan Vulovic / William Sheffler / Shally Saini / Yan Ting Zhao / Infencia Xavier Raj / Peter A Morawski / Madeleine F Jennewein / Leah J Homad / Yu-Hsin Wan / Marti R Tooley / Franziska Seeger / Ali Etemadi / Mitchell L Fahning / James Lazarovits / Alex Roederer / Alexandra C Walls / Lance Stewart / Mohammadali Mazloomi / Neil P King / Daniel J Campbell / Andrew T McGuire / Leonidas Stamatatos / Hannele Ruohola-Baker / Julie Mathieu / David Veesler / David Baker /
Abstract: Multivalent display of receptor-engaging antibodies or ligands can enhance their activity. Instead of achieving multivalency by attachment to preexisting scaffolds, here we unite form and function by ...Multivalent display of receptor-engaging antibodies or ligands can enhance their activity. Instead of achieving multivalency by attachment to preexisting scaffolds, here we unite form and function by the computational design of nanocages in which one structural component is an antibody or Fc-ligand fusion and the second is a designed antibody-binding homo-oligomer that drives nanocage assembly. Structures of eight nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage, respectively, closely match the corresponding computational models. Antibody nanocages targeting cell surface receptors enhance signaling compared with free antibodies or Fc-fusions in death receptor 5 (DR5)-mediated apoptosis, angiopoietin-1 receptor (Tie2)-mediated angiogenesis, CD40 activation, and T cell proliferation. Nanocage assembly also increases severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc-angiotensin-converting enzyme 2 (ACE2) fusion proteins.
History
DepositionJan 9, 2021-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.927
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.927
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23266.png

Downloads & links

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Map

FileDownload / File: emd_23266.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComputationally designed octahedral antibody nanocage with Fc o42.1+Fc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.927 / Movie #1: 0.927
Minimum - Maximum-0.5010544 - 3.5384045
Average (Standard dev.)-0.00026424203 (±0.23333134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.5013.538-0.000

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Supplemental data

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Sample components

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Entire : Computationally designed octahedral antibody nanocage with Fc o42.1+Fc

EntireName: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc
Components
  • Complex: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc

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Supramolecule #1: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc

SupramoleculeName: Computationally designed octahedral antibody nanocage with Fc o42.1+Fc
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.1 MDa

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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

Concentration0.8 mg/mL
BufferpH: 8
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4032
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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