9BJE | pdb_00009bje

Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Two-Component Pseudo-Icosahedral Protein Nanocompartment with Variable Shell Composition and Irregular Tiling.

Dutcher, C.A.Andreas, M.P.Giessen, T.W.

(2025) Adv Sci (Weinh) 12: e03617-e03617

  • DOI: https://doi.org/10.1002/advs.202503617
  • Primary Citation of Related Structures:  
    9BIX, 9BJE

  • PubMed Abstract: 

    Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral Hong Kong 97 (HK97)-fold. Here, the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus is reported. The differential assembly behavior of the two shell components and their ability to co-assemble into mixed shells with variable shell composition is demonstrated. The structures of both shell proteins are determined using cryo-electron microscopy. Using 3D-classification and cross-linking studies, the irregular tiling of mixed shells is highlighted. This work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.


  • Organizational Affiliation
    • Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Crp/Fnr family transcriptional regulator475Streptomyces lydicusMutation(s): 0 
Gene Names: ADL29_33315
UniProt
Find proteins for A0A0N0GW33 (Streptomyces chattanoogensis)
Explore A0A0N0GW33 
Go to UniProtKB:  A0A0N0GW33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N0GW33
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.2.0+210511
MODEL REFINEMENTCoot0.8.9.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133325

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-10
    Changes: Data collection, Database references