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- EMDB-12144: Brevibacterium linens encapsulin structure -

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Basic information

Entry
Database: EMDB / ID: EMD-12144
TitleBrevibacterium linens encapsulin structure
Map dataBrevibacterium linens encapsulin
Sample
  • Complex: Encapsulin
    • Protein or peptide: Linocin-M18
KeywordsBacterial protein compartment / STRUCTURAL PROTEIN
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Type 1 encapsulin shell protein
Function and homology information
Biological speciesBrevibacterium linens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsAllende-Ballestero C / Luque D
CitationJournal: To Be Published
Title: Three-dimensional cryoEM structure of Brevibacterium linens encapsulin
Authors: Allende-Ballestero C / Luque D / Klem R / Cornelissen JJLM / Caston JR
History
DepositionDec 21, 2020-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12144.png

Downloads & links

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Map

FileDownload / File: emd_12144.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBrevibacterium linens encapsulin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 314.1 Å		1.05 Å/pix.
x 300 pix.
= 314.1 Å		1.05 Å/pix.
x 300 pix.
= 314.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08102759 - 0.14881462
Average (Standard dev.)0.0006664659 (±0.009145229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 314.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Encapsulin

EntireName: Encapsulin
Components
  • Complex: Encapsulin
    • Protein or peptide: Linocin-M18

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Supramolecule #1: Encapsulin

SupramoleculeName: Encapsulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brevibacterium linens (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: Linocin-M18

MacromoleculeName: Linocin-M18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Brevibacterium linens (bacteria)
Molecular weightTheoretical: 28.590695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VNNLYRELAP IPGPAWAEIE EEARRTFKRN IAGRRIVDVA GPTGFETSAV TTGHIRDVQS ETSGLQVKQR IVQEYIELRT PFTVTRQAI DDVARGSGDS DWQPVKDAAT TIAMAEDRAI LHGLDAAGIG GIVPGSSNAA VAIPDAVEDF ADAVAQALSV L RTVGVDGP ...String:
VNNLYRELAP IPGPAWAEIE EEARRTFKRN IAGRRIVDVA GPTGFETSAV TTGHIRDVQS ETSGLQVKQR IVQEYIELRT PFTVTRQAI DDVARGSGDS DWQPVKDAAT TIAMAEDRAI LHGLDAAGIG GIVPGSSNAA VAIPDAVEDF ADAVAQALSV L RTVGVDGP YSLLLSSAEY TKVSESTDHG YPIREHLSRQ LGAGEIIWAP ALEGALLVST RGGDYELHLG QDLSIGYYSH DS ETVELYL QETFGFLALT DESSVPLSL

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
Component:
ConcentrationName
20.0 mMTris
150.0 mMAmmonium Chloride
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 38.85 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.0 µm
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: 309778
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3dkt

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 233829
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3)

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