Cryo-EM structure of the encapsulated DyP-type peroxidase from Mycobacterium smegmatis

Experimental Data Snapshot

  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin.

Tang, Y.Mu, A.Zhang, Y.Zhou, S.Wang, W.Lai, Y.Zhou, X.Liu, F.Yang, X.Gong, H.Wang, Q.Rao, Z.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2025658118
  • Primary Citation of Related Structures:  
    7BOJ, 7BOK

  • PubMed 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 and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis 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.

  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dyp-type peroxidase
A, B, C, D, E
A, B, C, D, E, F
343Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Find proteins for A0R4G9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R4G9 
Go to UniProtKB:  A0R4G9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R4G9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019
National Natural Science Foundation of China (NSFC)China813300237
Ministry of Science and Technology (MoST, China)China2017YFC0840300
Chinese Academy of SciencesChinaXDB08020200

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Refinement description