9FY6 | pdb_00009fy6

Single particle cryo-EM reconstruction of Bacillus Methanolicus encapsulin nano compartment

• PDB DOI: https://doi.org/10.2210/pdb9FY6/pdb
• EM Map EMD-50859: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bacillus methanolicus MGA3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-02 Released: 2025-06-11 
• Deposition Author(s): Marles-Wright, J., McIver, Z., Basle, A., Ross, J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Bacillus methanolicus encapsulin nano compartment

Marles-Wright, J., McIver, Z., Basle, A., Ross, J.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 240-mer - A240 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 128.2 kDa 
• Atom Count: 8,506 
• Modeled Residue Count: 1,059 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriocin	A, B, C, D	282	Bacillus methanolicus MGA3	Mutation(s): 0  Gene Names: BMMGA3_02020
UniProt
Find proteins for I3E3I1 (Bacillus methanolicus (strain MGA3 / ATCC 53907)) Explore I3E3I1  Go to UniProtKB:  I3E3I1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Marles-Wright, J., McIver, Z., Basle, A., Ross, J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	2306768
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N005570/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	1801041

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release