9FNA | pdb_00009fna

CryoEM structure of Encapsulin::tdNfsB with an open pore state

• PDB DOI: https://doi.org/10.2210/pdb9FNA/pdb
• EM Map EMD-50586: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-09 Released: 2025-03-19 
• Deposition Author(s): Capper, M.J., Kohhnke, J.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A nanoengineered tandem nitroreductase: designing a robust prodrug-activating nanoreactor.

Zmyslia, M., Capper, M.J., Grimmeisen, M., Sartory, K., Deuringer, B., Abdelsalam, M., Shen, K., Jung, M., Sippl, W., Koch, H.G., Kaul, L., Suss, R., Kohnke, J., Jessen-Trefzer, C.

(2024) RSC Chem Biol 6: 21-35

• PubMed: 39508026 
• DOI: https://doi.org/10.1039/d4cb00127c
• Primary Citation of Related Structures:  
  9FN9, 9FNA


• PubMed Abstract: 
  

  Nitroreductases are important enzymes for a variety of applications, including cancer therapy and bioremediation. They often require encapsulation to improve stability and activity. We focus on genetically encoded encapsulation of nitroreductases within protein capsids, like encapsulins. Our study showcases the encapsulation of nitroreductase NfsB as functional dimers within encapsulins, which enhances protein activity and stability in diverse conditions. Mutations within the pore region are beneficial for activity of the encapsulated enzyme, potentially by increasing diffusion rates. Cryogenic electron microscopy reveals the overall architecture of the encapsulated dimeric NfsB within the nanoreactor environment and identifies multiple pore states in the shell. These findings highlight the potential of encapsulins as versatile tools for enhancing enzyme performance across various fields.

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Organizational Affiliation: 
• Institute of Organic Chemistry, University of Freiburg 79104 Freiburg im Breisgau Germany [e-mail].
School of Chemistry, University of Glasgow Glasgow G12 8QQ UK [e-mail].
Institute of Pharmaceutical Science, Pharmaceutical Technology and Biopharmacy, University of Freiburg 79104 Freiburg im Breisgau Germany.
Department of Medicinal Chemistry, Martin-Luther University of Halle-Wittenberg 06120 Halle/Saale Germany.
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University Alexandria Egypt.
Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg 79104 Freiburg im Breisgau Germany.
Institute of Pharmaceutical Sciences, Chemical Epigenetics Group, University of Freiburg 79104 Freiburg im Breisgau Germany.
CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg Schänzlestrasse 18 79104 Freiburg im Breisgau Germany.
Institute of Food Chemistry, Leibniz University Hannover 30167 Hannover Germany.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,802.73 kDa 
• Atom Count: 121,020 
• Modeled Residue Count: 15,840 
• Deposited Residue Count: 16,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
29 kDa antigen Cfp29	A, AA [auth IB], AB [auth W], B [auth AA], BA [auth J], BB [auth WA], C [auth AB], CA [auth JA], CB [auth X], D [auth B], DA [auth K], DB [auth XA], E [auth BA], EA [auth KA], EB [auth Y], F [auth BB], FA [auth L], FB [auth YA], G [auth C], GA [auth LA], GB [auth Z], H [auth CA], HA [auth M], HB [auth ZA], I [auth CB], IA [auth MA], J [auth D], JA [auth N], K [auth DA], KA [auth NA], L [auth DB], LA [auth O], M [auth E], MA [auth OA], N [auth EA], NA [auth P], O [auth EB], OA [auth PA], P [auth F], PA [auth Q], Q [auth FA], QA, R [auth FB], RA [auth R], S [auth G], SA [auth RA], T [auth GA], TA [auth S], U [auth GB], UA [auth SA], V [auth H], VA [auth T], W [auth HA], WA [auth TA], X [auth HB], XA [auth UA], Y [auth I], YA [auth V], Z [auth IA], ZA [auth VA]	275	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: MSMEG_5830
UniProt
Find proteins for I6WZG6 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6WZG6  Go to UniProtKB:  I6WZG6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Capper, M.J., Kohhnke, J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101002326

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release