[English] 日本語
Yorodumi- PDB-8tk7: Myxococcus xanthus EncA protein shell with compartmentalized SNAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tk7 | ||||||
---|---|---|---|---|---|---|---|
Title | Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein | ||||||
Components |
| ||||||
Keywords | VIRUS LIKE PARTICLE / Encapsulin / nanocompartment | ||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / methylation / DNA repair / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Myxococcus xanthus DK 1622 (bacteria) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||
Authors | Andreas, M.P. / Kwon, S. / Giessen, T.W. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J Struct Biol / Year: 2023 Title: Structure and heterogeneity of a highly cargo-loaded encapsulin shell. Authors: Seokmu Kwon / Michael P Andreas / Tobias W Giessen / Abstract: Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in ...Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tk7.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tk7.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tk7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8tk7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8tk7_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 8tk7_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/8tk7 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/8tk7 | HTTPS FTP |
-Related structure data
Related structure data | 41322MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 31691.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: encA, MXAN_3556 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1D6H4 #2: Protein | Mass: 21482.600 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Amino acids 1-183 are unresolved SNAP-TAG. Amino acids 184-191 are unresolved linker. Amino acids 192-203 are EncC targeting peptide. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5BBQ0 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 150 mM NaCl, 20 mM Tris pH 7.5 | ||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||
Specimen | Conc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.2 sec. / Electron dose: 49.26 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2610 |
Image scans | Width: 4092 / Height: 5760 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50680 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 89.9 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: The model was initially fit into the map using UCSF ChimeraX. It was then manually refined using Coot, followed by real-space refinement against the map using Phenix. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7S2T Accession code: 7S2T / Source name: PDB / Type: experimental model |