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- EMDB-72682: Cryo-EM structure of Thermotoga maritima encapsulin shell -

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Basic information

Entry
Database: EMDB / ID: EMD-72682
TitleCryo-EM structure of Thermotoga maritima encapsulin shell
Map dataEncapsulin map density
Sample
  • Complex: Cryo-EM structure of Thermotoga maritima encapsulin shell
    • Protein or peptide: Type 1 encapsulin shell protein
KeywordsENCAPSULIN SHELL / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / iron ion transport / peptidase activity / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / :
Similarity search - Domain/homology
Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTorres VJ / Vera CS / Cisneros YW / Portugal RV / Guerra DG / Evangelista W
Funding support Peru, 2 items
OrganizationGrant numberCountry
Other governmentPROCIENCIA PE501080175-2022 Peru
Other governmentPROCIENCIA PE501089887-2024-PROCIENCIA Peru
CitationJournal: To Be Published
Title: Cryo-EM structure of Thermotoga maritima encapsulin shell
Authors: Torres VJ / Vera CS / Cisneros YW / Portugal RV / Guerra DG / Evangelista W
History
DepositionSep 11, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72682.png

Downloads & links

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Map

FileDownload / File: emd_72682.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEncapsulin map density
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 520 pix.
= 575.64 Å		1.11 Å/pix.
x 520 pix.
= 575.64 Å		1.11 Å/pix.
x 520 pix.
= 575.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.107 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.542
Minimum - Maximum-0.21071468 - 1.1490185
Average (Standard dev.)0.00030255853 (±0.06099531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 575.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_72682_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72682_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Thermotoga maritima encapsulin shell

EntireName: Cryo-EM structure of Thermotoga maritima encapsulin shell
Components
  • Complex: Cryo-EM structure of Thermotoga maritima encapsulin shell
    • Protein or peptide: Type 1 encapsulin shell protein

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Supramolecule #1: Cryo-EM structure of Thermotoga maritima encapsulin shell

SupramoleculeName: Cryo-EM structure of Thermotoga maritima encapsulin shell
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Thermotoga maritima encapsulin shell expressed by E. coli
Source (natural)Organism: Thermotoga maritima (bacteria)

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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: 60 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 30.516787 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY ...String:
MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY TLVINTDRWI NFLKEEAGHY PLEKRVEECL RGGKIITTPR IEDALVVSER GGDFKLILGQ DLSIGYEDRE KD AVRLFIT ETFTFQVVNP EALILLKF

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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3dkt

Final reconstructionNumber classes used: 7 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 46110
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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