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- EMDB-19521: Q. thermotolerans Engineered Encapsulin P3P4 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19521
TitleQ. thermotolerans Engineered Encapsulin P3P4
Map dataSharp map from CryoSPARC refinement.
Sample
  • Complex: Engineered Encapsulin P3P4
KeywordsEncapsulin / Nanocage / Compartment / Storage / Complex / VIRUS LIKE PARTICLE
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein
Function and homology information
Biological speciesBacillus thermotolerans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSatler T / Jerala R
Funding support Slovenia, 1 items
OrganizationGrant numberCountry
Slovenian Research AgencyP4-0176 Slovenia
CitationJournal: To Be Published
Title: Structure of engineered encapsulin P3P4
Authors: Satler T / Jerala R
History
DepositionJan 31, 2024-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19521.png

Downloads & links

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Map

FileDownload / File: emd_19521.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map from CryoSPARC refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 540 pix.
= 648. Å		1.2 Å/pix.
x 540 pix.
= 648. Å		1.2 Å/pix.
x 540 pix.
= 648. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.03
Minimum - Maximum-2.4978466 - 4.845316
Average (Standard dev.)0.0020438333 (±0.26494208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19521_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Basic map from CryoSPARC refinement.

Fileemd_19521_additional_1.map
AnnotationBasic map from CryoSPARC refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from CryoSPARC reinement.

Fileemd_19521_half_map_1.map
AnnotationHalf map 1 from CryoSPARC reinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from CryoSPARC reinement.

Fileemd_19521_half_map_2.map
AnnotationHalf map 2 from CryoSPARC reinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Engineered Encapsulin P3P4

EntireName: Engineered Encapsulin P3P4
Components
  • Complex: Engineered Encapsulin P3P4

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Supramolecule #1: Engineered Encapsulin P3P4

SupramoleculeName: Engineered Encapsulin P3P4 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus thermotolerans (bacteria)

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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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.9 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 3082
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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