9B9Q | pdb_00009b9q

Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Pore Engineering as a General Strategy to Improve Protein-Based Enzyme Nanoreactor Performance.

Kwon, S.Andreas, M.P.Giessen, T.W.

(2024) ACS Nano 18: 25740-25753

  • DOI: https://doi.org/10.1021/acsnano.4c08186
  • Primary Citation of Related Structures:  
    9B9I, 9B9Q, 9BC8

  • PubMed Abstract: 

    Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and colocalization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins-microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for diverse future biotechnological and biomedical applications.


  • Organizational Affiliation
    • Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type 1 encapsulin shell protein EncA
A, B, C
281Myxococcus xanthus DK 1622Mutation(s): 2 
Gene Names: encAMXAN_3556
UniProt
Find proteins for Q1D6H4 (Myxococcus xanthus (strain DK1622))
Explore Q1D6H4 
Go to UniProtKB:  Q1D6H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1D6H4
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Encapsulin nanocompartment cargo protein EncCD [auth F],
E [auth G],
F [auth H]
12Myxococcus xanthus DK 1622Mutation(s): 0 
Gene Names: encCMXAN_4464
UniProt
Find proteins for Q1D3Y8 (Myxococcus xanthus (strain DK1622))
Explore Q1D3Y8 
Go to UniProtKB:  Q1D3Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1D3Y8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.10.0
MODEL REFINEMENTPHENIXv1.20.1-4487-000
MODEL REFINEMENTCootv0.9.8.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133325-05

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Database references