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Yorodumi- PDB-8ika: Cryo-EM structure of the encapsulin shell from Mycobacterium tube... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ika | ||||||||||||
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Title | Cryo-EM structure of the encapsulin shell from Mycobacterium tuberculosis | ||||||||||||
Components | Type 1 encapsulin shell protein | ||||||||||||
Keywords | VIRUS LIKE PARTICLE / CFP-29 / Mycobacterium tuberculosis / cryo-EM / encapsulin | ||||||||||||
Function / homology | : / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein Function and homology information | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||||||||
Authors | Du, Z. / Lai, Y. / Gao, Y. / Rao, Z. / Gong, H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Structure of mycobacterium tuberculosis encapsulin Authors: Du, Z. / Lai, Y. / Gao, Y. / Rao, Z. / Gong, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ika.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ika.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ika.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ika ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ika | HTTPS FTP |
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-Related structure data
Related structure data | 35507MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: enc, cfp29, Rv0798c / Production host: Escherichia coli (E. coli) / References: UniProt: I6WZG6 |
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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 |
-Sample preparation
Component | Name: Mycobacterium tuberculosis encapsulin / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2 MDa / Experimental value: YES |
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251715 / Symmetry type: POINT |