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- EMDB-43042: Myxococcus xanthus HEnc-K417N(A) protein shell with D2 symmetry (... -

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Basic information

Entry
Database: EMDB / ID: EMD-43042
TitleMyxococcus xanthus HEnc-K417N(A) protein shell with D2 symmetry (12 pentamers, 14 hexamers)
Map data
Sample
  • Complex: Myxococcus xanthus EncA protein modified with a his-tag and K417N(A) insertion: icosahedral T1 shell
Keywordsencapsulin / nanocompartment / nanoparticle / cage / STRUCTURAL PROTEIN
Biological speciesMyxococcus xanthus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.08 Å
AuthorsHernandez C / Jenkins MC / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: bioRxiv / Year: 2024
Title: Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing.
Authors: Sonia Bhattacharya / Matthew C Jenkins / Parisa Keshavarz-Joud / Alisyn Retos Bourque / Keiyana White / Amina M Alvarez Barkane / Anton V Bryksin / Carolina Hernandez / Mykhailo Kopylov / M G Finn /
Abstract: Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments ...Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from were designed to package bacterial RNA when produced in and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.
History
DepositionDec 5, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43042.png

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Map

FileDownload / File: emd_43042.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.408 Å
Density
Contour LevelBy AUTHOR: 2.18
Minimum - Maximum-1.3584678 - 4.567895
Average (Standard dev.)-0.021301491 (±0.46798822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 616.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43042_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_43042_half_map_1.map
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Half map: #2

Fileemd_43042_half_map_2.map
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Sample components

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Entire : Myxococcus xanthus EncA protein modified with a his-tag and K417N...

EntireName: Myxococcus xanthus EncA protein modified with a his-tag and K417N(A) insertion: icosahedral T1 shell
Components
  • Complex: Myxococcus xanthus EncA protein modified with a his-tag and K417N(A) insertion: icosahedral T1 shell

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Supramolecule #1: Myxococcus xanthus EncA protein modified with a his-tag and K417N...

SupramoleculeName: Myxococcus xanthus EncA protein modified with a his-tag and K417N(A) insertion: icosahedral T1 shell
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Myxococcus xanthus (bacteria)
Molecular weightTheoretical: 4.875 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

Concentration4.2 mg/mL
BufferpH: 8.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: 10 second wait, 1 second blot.

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2971 / Average exposure time: 1.0 sec. / Average electron dose: 50.0 e/Å2
Details: NYSBC session m23aug21f, px size 1.204 A, 25 frames

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Image processing

Particle selectionNumber selected: 285341
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 9292
FSC plot (resolution estimation)

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