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- PDB-8pys: Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pys | ||||||
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Title | Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocompartment from Mycobacterium tuberculosis with icosahedral symmetry imposed. | ||||||
![]() | 29 kDa antigen CFP29 | ||||||
![]() | VIRUS LIKE PARTICLE / Encapsulin / cfp29 / nanocompartment | ||||||
Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
![]() | Willmore, R. / Woodward, J.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin nanocompartment containing DyP peroxidase. Authors: Willmore, R. / Woodward, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 327 KB | Display | |
Data in CIF | ![]() | 456.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18031MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 29554.072 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cfp29, Rv0798c / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: DyP cargo loaded encapsulin nanocompartment / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Cryogen name: NITROGEN |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6204 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 150444 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121235 / Num. of class averages: 6 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 26.39 / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7BOJ Pdb chain-ID: A / Accession code: 7BOJ / Source name: PDB / Type: experimental model |