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- EMDB-51500: Partial (48mer) encapsulin shell assembly from Mycobacterium tube... -

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Basic information

Entry
Database: EMDB / ID: EMD-51500
TitlePartial (48mer) encapsulin shell assembly from Mycobacterium tuberculosis
Map datapostprocess unmasked
Sample
  • Organelle or cellular component: Partial encapsulin shell from Mycobacterium tuberculosis
    • Protein or peptide: Type 1 encapsulin shell protein
Keywordsencapsulin / VIRUS LIKE PARTICLE
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.42 Å
AuthorsLewis CJ / Berger C / Ravelli RBG
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
Other governmentLHSM18067
CitationJournal: Commun Biol / Year: 2025
Title: In situ and in vitro cryo-EM reveal structures of mycobacterial encapsulin assembly intermediates.
Authors: Casper Berger / Chris Lewis / Ye Gao / Kèvin Knoops / Carmen López-Iglesias / Peter J Peters / Raimond B G Ravelli /
Abstract: Prokaryotes rely on proteinaceous compartments such as encapsulin to isolate harmful reactions. Encapsulin are widely expressed by bacteria, including the Mycobacteriaceae, which include the human ...Prokaryotes rely on proteinaceous compartments such as encapsulin to isolate harmful reactions. Encapsulin are widely expressed by bacteria, including the Mycobacteriaceae, which include the human pathogens Mycobacterium tuberculosis and Mycobacterium leprae. Structures of fully assembled encapsulin shells have been determined for several species, but encapsulin assembly and cargo encapsulation are still poorly characterised, because of the absence of encapsulin structures in intermediate assembly states. We combine in situ and in vitro structural electron microscopy to show that encapsulins are dynamic assemblies with intermediate states of cargo encapsulation and shell assembly. Using cryo-focused ion beam (FIB) lamella preparation and cryo-electron tomography (CET), we directly visualise encapsulins in Mycobacterium marinum, and observed ribbon-like attachments to the shell, encapsulin shells with and without cargoes, and encapsulin shells in partially assembled states. In vitro cryo-electron microscopy (EM) single-particle analysis of the Mycobacterium tuberculosis encapsulin was used to obtain three structures of the encapsulin shell in intermediate states, as well as a 2.3 Å structure of the fully assembled shell. Based on the analysis of the intermediate encapsulin shell structures, we propose a model of encapsulin self-assembly via the pairwise addition of monomers.
History
DepositionSep 6, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51500.png

Downloads & links

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Map

FileDownload / File: emd_51500.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess unmasked
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 320.256 Å		0.83 Å/pix.
x 384 pix.
= 320.256 Å		0.83 Å/pix.
x 384 pix.
= 320.256 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
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Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.007466861 - 0.021546435
Average (Standard dev.)0.00012090082 (±0.0024981021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 320.25598 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51500_msk_1.map
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Additional map: 48mer post-process masked

Fileemd_51500_additional_1.map
Annotation48mer post-process masked
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Half map: halfmap2

Fileemd_51500_half_map_1.map
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Fileemd_51500_half_map_2.map
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Sample components

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Entire : Partial encapsulin shell from Mycobacterium tuberculosis

EntireName: Partial encapsulin shell from Mycobacterium tuberculosis
Components
  • Organelle or cellular component: Partial encapsulin shell from Mycobacterium tuberculosis
    • Protein or peptide: Type 1 encapsulin shell protein

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Supramolecule #1: Partial encapsulin shell from Mycobacterium tuberculosis

SupramoleculeName: Partial encapsulin shell from Mycobacterium tuberculosis
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 48 of 60 monomers
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: Rv0798c

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Macromolecule #1: Type 1 encapsulin shell protein

MacromoleculeName: Type 1 encapsulin shell protein / type: protein_or_peptide / ID: 1 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 28.863346 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNNLYRDLAP VTEAAWAEIE LEAARTFKRH IAGRRVVDVS DPGGPVTAAV STGRLIDVKA PTNGVIAHLR ASKPLVRLRV PFTLSRNEI DDVERGSKDS DWEPVKEAAK KLAFVEDRTI FEGYSAASIE GIRSASSNPA LTLPEDPREI PDVISQALSE L RLAGVDGP ...String:
MNNLYRDLAP VTEAAWAEIE LEAARTFKRH IAGRRVVDVS DPGGPVTAAV STGRLIDVKA PTNGVIAHLR ASKPLVRLRV PFTLSRNEI DDVERGSKDS DWEPVKEAAK KLAFVEDRTI FEGYSAASIE GIRSASSNPA LTLPEDPREI PDVISQALSE L RLAGVDGP YSVLLSADVY TKVSETSDHG YPIREHLNRL VDGDIIWAPA IDGAFVLTTR GGDFDLQLGT DVAIGYASHD TD TVRLYLQ ETLTFLCYTA EASVALSH

UniProtKB: Type 1 encapsulin shell 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

Concentration2.5 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 163000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 89072
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7p1t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3427
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7p1t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9got:
Partial (48mer) encapsulin shell assembly from Mycobacterium tuberculosis

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