[English] 日本語
![](img/lk-miru.gif)
- PDB-7bok: Cryo-EM structure of the encapsulated DyP-type peroxidase from My... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bok | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the encapsulated DyP-type peroxidase from Mycobacterium smegmatis | |||||||||||||||
![]() | Dyp-type peroxidase | |||||||||||||||
![]() | OXIDOREDUCTASE / Cargo protein / Dodecamer / Heme-containing enzyme | |||||||||||||||
Function / homology | Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Tang, Y.T. / Mu, A. / Gong, H.R. / Wang, Q. / Rao, Z.H. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Cryo-EM structure of DyP-loaded encapsulin. Authors: Yanting Tang / An Mu / Yuying Zhang / Shan Zhou / Weiwei Wang / Yuezheng Lai / Xiaoting Zhou / Fengjiang Liu / Xiuna Yang / Hongri Gong / Quan Wang / Zihe Rao / ![]() Abstract: Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact ...Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery. | |||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 320.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 264.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 30131MC ![]() 7bojC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 | ![]()
|
2 |
|
3 | ![]()
|
Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
-
Components
#1: Protein | Mass: 37252.340 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7GEX3, peroxidase #2: Chemical | ChemComp-HEM / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Encapsulin from Mycobacterium smegmatis / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6.4 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-
Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13937 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 4GU7 Accession code: 4GU7 / Source name: PDB / Type: experimental model |