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- EMDB-18031: Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocom... -

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Basic information

Entry
Database: EMDB / ID: EMD-18031
TitleCryo-EM structure of the DyP peroxidase-loaded encapsulin nanocompartment from Mycobacterium tuberculosis with icosahedral symmetry imposed.
Map dataThe 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin containing DyP peroxidase
Sample
  • Organelle or cellular component: DyP cargo loaded encapsulin nanocompartment
    • Protein or peptide: 29 kDa antigen CFP29
KeywordsEncapsulin / cfp29 / nanocompartment / 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 H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWillmore R / Woodward JD
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Global Challenges Research Fund United Kingdom
CitationJournal: To Be Published
Title: The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin nanocompartment containing DyP peroxidase.
Authors: Willmore R / Woodward JD
History
DepositionJul 26, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18031.png

Downloads & links

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Map

FileDownload / File: emd_18031.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin containing DyP peroxidase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.056045763 - 0.08954841
Average (Standard dev.)0.00008923478 (±0.0042135357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_18031_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_18031_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DyP cargo loaded encapsulin nanocompartment

EntireName: DyP cargo loaded encapsulin nanocompartment
Components
  • Organelle or cellular component: DyP cargo loaded encapsulin nanocompartment
    • Protein or peptide: 29 kDa antigen CFP29

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Supramolecule #1: DyP cargo loaded encapsulin nanocompartment

SupramoleculeName: DyP cargo loaded encapsulin nanocompartment / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: 29 kDa antigen CFP29

MacromoleculeName: 29 kDa antigen CFP29 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 29.554072 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (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 EASVALSHHH HHH

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: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-HCl
350.0 mMNaClSodium chloride
10.0 mMC3H4N2Imidazole
10.0 v/vC3H8O3Glycerol
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6204 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 150444
Startup modelType of model: NONE
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0.) / Number images used: 121235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0.)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1.0.)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7boj


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 26.39 / Target criteria: Cross-correlation coefficient
Output model

PDB-8pys:
Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocompartment from Mycobacterium tuberculosis with icosahedral symmetry imposed.

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