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Open data
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Basic information
Entry | Database: PDB / ID: 7p1t | |||||||||
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Title | Cryo-EM structure of encapsulin from Mycobacterium tuberculosis | |||||||||
![]() | 29 kDa antigen, Cfp29 | |||||||||
![]() | VIRUS LIKE PARTICLE / encapsulin / cfp29 / nanocompartment | |||||||||
Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / defense response to bacterium / 29 kDa antigen, Cfp29![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å | |||||||||
![]() | Lewis, C.J. / Berger, C. / Ravelli, R.B.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Encapsulins in mycobacteria: from single particle to in situ Authors: Lewis, C.J. / Berger, C. / Gao, Y. / Lopez-Iglesias, C. / Peters, P.J. / Ravelli, R.B.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 300.4 KB | Display | |
Data in CIF | ![]() | 360.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13164MC 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: 28863.346 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cfp29, lin, C0094_04325, CAB90_00906, DSI38_23045, E5M05_20280, E5M52_19875, E5M78_19835, ERS007661_02029, ERS007665_01536, ERS007679_03499, ERS007688_03248, ERS007741_01530, ERS013471_03708, ...Gene: cfp29, lin, C0094_04325, CAB90_00906, DSI38_23045, E5M05_20280, E5M52_19875, E5M78_19835, ERS007661_02029, ERS007665_01536, ERS007679_03499, ERS007688_03248, ERS007741_01530, ERS013471_03708, ERS023446_03804, ERS027659_01280, ERS094182_03983, F6W99_03480, FRD82_02930, GCL30_20955, SAMEA2683035_02949 Production host: ![]() ![]() References: UniProt: A0A045HTX8, Hydrolases; Acting on peptide bonds (peptidases) |
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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: encapsulin shell from Mycobacterium tuberculosis / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.729 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % |
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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: 163000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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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: 89072 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57805 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 34.36 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: multiple | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 619G |