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- EMDB-43036: Myxococcus xanthus HEnc-K417N(A) protein shell with icosahedral T... -

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Basic information

Entry
Database: EMDB / ID: EMD-43036
TitleMyxococcus xanthus HEnc-K417N(A) protein shell with icosahedral T=3 symmetry
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: 4.91 Å
AuthorsHernandez C / Jenkins MC / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing
Authors: Bhattacharya S / Jenkins MC / Keshavarz-Joud P / Bourque AR / White K / Alvarez Barkane AM / Bryksin A / Hernandez C / Kopylov M / Finn MG
History
DepositionDec 5, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43036.png

Downloads & links

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Map

FileDownload / File: emd_43036.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.41 Å/pix.
x 256 pix.
= 616.448 Å		2.41 Å/pix.
x 256 pix.
= 616.448 Å		2.41 Å/pix.
x 256 pix.
= 616.448 Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.72
Minimum - Maximum-1.2084877 - 5.9753633
Average (Standard dev.)-0.011171727 (±0.57420236)
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_43036_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_43036_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43036_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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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: 6.094 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
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
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: 3.0 µm / Nominal defocus min: 1.5 µm

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Image processing

Particle selectionNumber selected: 285341
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 71580
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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