9ZVV | pdb_00009zvv

Quasibacillus thermotolerans T=4 encapsulin pore mutant variant Glass 9

• PDB DOI: https://doi.org/10.2210/pdb9ZVV/pdb
• EM Map EMD-74892: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Bacillus thermotolerans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-30 Released: 2026-07-01 
• Deposition Author(s): Andreas, M.P., Siddiquee, R., Giessen, T.W., Lau, Y.H.
• Funding Organization(s): Australian Research Council (ARC), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Directed evolution of multimeric proteins is enabled by dual-compensatory gene duplication.

Siddiquee, R., Lie, F., Szyszka, T.N., Loustau, A., Andreas, M.P., Giessen, T.W., Lau, Y.H.

(2026) bioRxiv 

• PubMed: 41648261 
• DOI: https://doi.org/10.64898/2026.01.12.698938
• Primary Citation Related Structures: 
  9ZVV, 9ZW3, 9ZW4


• PubMed Abstract: 
  

  Gene duplication has played a critical role in the evolutionary history of proteins, enabling complex multimers to emerge from simpler precursors. Yet in protein engineering, current methods for directed evolution do not exploit gene duplication, hampering access to the vast array of diverse variants that are only enriched in the presence of a wild-type copy. We establish a directed evolution strategy for multimeric proteins that harnesses gene duplication to compensate for metabolic burden and self-assembly fitness, allowing previously inaccessible variants to be enriched. Starting from a homomeric 240-mer capsid, gene duplication enables selection of both extreme homomeric variants and obligate heteromers. This strategy significantly expands engineering access to diverse high-performing variants, while also supporting a plausible model for evolutionary diversification of higher-order multimers in nature.

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Organizational Affiliation: 
• School of Chemistry, The University of Sydney; Camperdown, NSW 2006, Australia.
The University of Sydney Nano Institute, The University of Sydney; Camperdown, NSW 2006, Australia.
ARC Centre of Excellence in Synthetic Biology, The University of Sydney; Camperdown, NSW 2006, Australia.
Department of Biological Chemistry, University of Michigan Medical School; Ann Arbor, MI 48109, USA.
ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney; Camperdown, NSW 2006, Australia.

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, gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 124.83 kDa 
• Atom Count: 8,460 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 1 encapsulin shell protein	A, B, C [auth D], D [auth C]	279	Bacillus thermotolerans	Mutation(s): 0  Gene Names: enc, QY95_01592
UniProt
Find proteins for A0A0F5HPP7 (Bacillus thermotolerans) Explore A0A0F5HPP7  Go to UniProtKB:  A0A0F5HPP7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	Coot	0.9.8.1
MODEL REFINEMENT	PHENIX	1.20.1-4487-000

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Andreas, M.P., Siddiquee, R., Giessen, T.W., Lau, Y.H.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP230101045
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133325
National Science Foundation (NSF, United States)	United States	2342136

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release