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- EMDB-13164: Cryo-EM structure of encapsulin from Mycobacterium tuberculosis -

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Basic information

Entry
Database: EMDB / ID: EMD-13164
TitleCryo-EM structure of encapsulin from Mycobacterium tuberculosis
Map dataLocSpiral map
Sample
  • Organelle or cellular component: encapsulin shell from Mycobacterium tuberculosis
    • 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 / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity / 29 kDa antigen, Cfp29
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsLewis CJ / Berger C
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
Other governmentLHSM18067 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: To Be Published
Title: Encapsulins in mycobacteria: from single particle to in situ
Authors: Lewis CJ / Berger C / Gao Y / Lopez-Iglesias C / Peters PJ / Ravelli RBG
History
DepositionJul 2, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13164.png

Downloads & links

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Map

FileDownload / File: emd_13164.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocSpiral map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.8
Minimum - Maximum0.0 - 29.838861000000001
Average (Standard dev.)0.43837747 (±1.7970632)
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_13164_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: relion postprocess masked

Fileemd_13164_additional_1.map
Annotationrelion postprocess masked
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap

Fileemd_13164_half_map_1.map
Annotationhalfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap

Fileemd_13164_half_map_2.map
Annotationhalfmap
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : encapsulin shell from Mycobacterium tuberculosis

EntireName: encapsulin shell from Mycobacterium tuberculosis
Components
  • Organelle or cellular component: encapsulin shell from Mycobacterium tuberculosis
    • Protein or peptide: 29 kDa antigen, Cfp29

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Supramolecule #1: encapsulin shell from Mycobacterium tuberculosis

SupramoleculeName: encapsulin shell from Mycobacterium tuberculosis / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 1.729 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 / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Mycobacterium tuberculosis (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: 29 kDa antigen, Cfp29

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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 / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / 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 exposure time: 1.8 sec. / 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57805
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:

619g


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 34.36 / Target criteria: multiple
Output model

PDB-7p1t:
Cryo-EM structure of encapsulin from Mycobacterium tuberculosis

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