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- EMDB-52715: Structure of Encapsulin from Dendrosporobacter quercicolus -

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Basic information

Entry
Database: EMDB / ID: EMD-52715
TitleStructure of Encapsulin from Dendrosporobacter quercicolus
Map data
Sample
  • Complex: Encapsulin
    • Protein or peptide: Encapsulin
KeywordsEncapsulin / CYTOSOLIC PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesDendrosporobacter quercicolus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBelyy A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Encapsulin from Dendrosporobacter quercicolus
Authors: Pecanac O / Belyy A / Martin C / Kleissen R / Fraaije M / Loncar N
History
DepositionFeb 4, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52715.png

Downloads & links

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Map

FileDownload / File: emd_52715.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 440 pix.
= 698.896 Å		1.59 Å/pix.
x 440 pix.
= 698.896 Å		1.59 Å/pix.
x 440 pix.
= 698.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5884 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-0.41055217 - 2.1411312
Average (Standard dev.)0.011618501 (±0.14273852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 698.896 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52715_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_52715_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52715_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52715_half_map_2.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 : Encapsulin

EntireName: Encapsulin
Components
  • Complex: Encapsulin
    • Protein or peptide: Encapsulin

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Supramolecule #1: Encapsulin

SupramoleculeName: Encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dendrosporobacter quercicolus (bacteria)

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Macromolecule #1: Encapsulin

MacromoleculeName: Encapsulin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Dendrosporobacter quercicolus (bacteria)
Molecular weightTheoretical: 30.03125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFLDRNAAP LNEGEWQRID EAVVSTARRT LVARRIIDVL GPLGSGVYSI PYSVFSGKSP TGIDMVGENE EFVVEASRRA TINLPILYK DFKIMWRDVE ADRHLGLPID VSTAAVAGNF VAVQEDHLIF NGNVELGHDG LFTVKDRQTV AISDWNETGA A LADVVKAV ...String:
MDFLDRNAAP LNEGEWQRID EAVVSTARRT LVARRIIDVL GPLGSGVYSI PYSVFSGKSP TGIDMVGENE EFVVEASRRA TINLPILYK DFKIMWRDVE ADRHLGLPID VSTAAVAGNF VAVQEDHLIF NGNVELGHDG LFTVKDRQTV AISDWNETGA A LADVVKAV GALSQAGHYG PYAMVVSPVL FGRMIRVFGN TGMLELDQVK ALITGGVHYS NVIGGSKAVV VATGSQNLNL AL GQDMVTA YMGPTSMNHV FRVLETAALL VRRPDAICTI E

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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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