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- EMDB-16401: GRM3C BMC shell from R. palustris, T=4 -

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Basic information

Entry
Database: EMDB / ID: EMD-16401
TitleGRM3C BMC shell from R. palustris, T=4
Map dataPostprocessed map, hand inverted compared to half-maps
Sample
  • Organelle or cellular component: Bacterial microcompartment shell from Rhodopseudomonas palustris BisB18
KeywordsBacterial microcompartment / BMC shell / GRM3 / STRUCTURAL PROTEIN
Biological speciesRhodopseudomonas palustris BisB18 (phototrophic)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGreber BJ / Ferlez BH / Kirst H / Sutter M / Nogales E / Kerfeld CA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI114975-06 United States
Department of Energy (DOE, United States)DE-SC0023395 United States
CitationJournal: Adv Mater / Year: 2023
Title: Heterologous Assembly of Pleomorphic Bacterial Microcompartment Shell Architectures Spanning the Nano- to Microscale.
Authors: Bryan H Ferlez / Henning Kirst / Basil J Greber / Eva Nogales / Markus Sutter / Cheryl A Kerfeld /
Abstract: Many bacteria use protein-based organelles known as bacterial microcompartments (BMCs) to organize and sequester sequential enzymatic reactions. Regardless of their specialized metabolic function, ...Many bacteria use protein-based organelles known as bacterial microcompartments (BMCs) to organize and sequester sequential enzymatic reactions. Regardless of their specialized metabolic function, all BMCs are delimited by a shell made of multiple structurally redundant, yet functionally diverse, hexameric (BMC-H), pseudohexameric/trimeric (BMC-T), or pentameric (BMC-P) shell protein paralogs. When expressed without their native cargo, shell proteins have been shown to self-assemble into 2D sheets, open-ended nanotubes, and closed shells of ≈40 nm diameter that are being developed as scaffolds and nanocontainers for applications in biotechnology. Here, by leveraging a strategy for affinity-based purification, it is demonstrated that a wide range of empty synthetic shells, many differing in end-cap structures, can be derived from a glycyl radical enzyme-associated microcompartment. The range of pleomorphic shells observed, which span ≈2 orders of magnitude in size from ≈25 nm to ≈1.8 µm, reveal the remarkable plasticity of BMC-based biomaterials. In addition, new capped nanotube and nanocone morphologies are observed that are consistent with a multicomponent geometric model in which architectural principles are shared among asymmetric carbon, viral protein, and BMC-based structures.
History
DepositionDec 23, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16401.png

Downloads & links

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Map

FileDownload / File: emd_16401.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map, hand inverted compared to half-maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 288 pix.
= 404.064 Å		1.4 Å/pix.
x 288 pix.
= 404.064 Å		1.4 Å/pix.
x 288 pix.
= 404.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.059552394 - 0.11017012
Average (Standard dev.)0.00029664923 (±0.008111562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 404.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Gold-standard refinement half map

Fileemd_16401_half_map_1.map
AnnotationGold-standard refinement half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gold-standard refinement half map

Fileemd_16401_half_map_2.map
AnnotationGold-standard refinement half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial microcompartment shell from Rhodopseudomonas palustris ...

EntireName: Bacterial microcompartment shell from Rhodopseudomonas palustris BisB18
Components
  • Organelle or cellular component: Bacterial microcompartment shell from Rhodopseudomonas palustris BisB18

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Supramolecule #1: Bacterial microcompartment shell from Rhodopseudomonas palustris ...

SupramoleculeName: Bacterial microcompartment shell from Rhodopseudomonas palustris BisB18
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Rhodopseudomonas palustris BisB18 (phototrophic)
Molecular weightTheoretical: 2.4 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

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES-NaOH
50.0 mMSodium chlorideNaCl
0.01 %Nonidet P40 (NP-40)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 3 / Support film - #0 - Material: GOLD / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 4 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number real images: 378 / #0 - Average electron dose: 25.0 e/Å2
#0 - Details: Images collected on carbon-coated holey carbon grid.
#1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number real images: 724 / #1 - Average electron dose: 25.0 e/Å2
#1 - Details: Images collected on carbon-coated holey gold grid.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 35638 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Image recording ID1
DetailsCombined dataset from all collected micrographs.
Particle selectionNumber selected: 90863
Startup modelType of model: EMDB MAP
EMDB ID:

9309


Details: Size of icosahedral starting map adjusted to match approximate particle diameter.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: Final reconstruction from symmetry expanded dataset (60 x 964 = 75,840 particles)
Number images used: 964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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