Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 540-mer - A540 

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

Macromolecule Content

• Total Structure Weight: 261.68 kDa 
• Atom Count: 18,333 
• Modelled Residue Count: 2,448 
• Deposited Residue Count: 2,457 
• Unique protein chains: 1

 8E16

Mycobacterium phage Che8

• PDB DOI:  https://doi.org/10.2210/pdb8E16/pdb
• EM Map EMD-27824: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Mycobacterium virus Che8
• Mutation(s): No 


• Deposited: 2022-08-09 Released: 2023-02-01 
• Deposition Author(s): Podgorski, J.M., White, S.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.

Podgorski, J.M., Freeman, K., Gosselin, S., Huet, A., Conway, J.F., Bird, M., Grecco, J., Patel, S., Jacobs-Sera, D., Hatfull, G., Gogarten, J.P., Ravantti, J., White, S.J.

(2023) Structure 31: 282

• PubMed: 36649709 
• DOI: https://doi.org/10.1016/j.str.2022.12.012
• Primary Citation of Related Structures:  
  8E16, 8EB4, 8EC2, 8EC8, 8ECI, 8ECJ, 8ECK, 8ECN, 8ECO, 8EDU


• PubMed Abstract: 
  

Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. After the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination of 10 capsids, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. We show that the actinobacteriophage major capsid proteins can be classified into 15 groups based upon their HK97-fold.

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Organizational Affiliation: 

Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein, gp6	A [auth I], B [auth A], C [auth G], D [auth F], E, F [auth B], G [auth C], H [auth D], I [auth H]	273	Mycobacterium virus Che8	Mutation(s): 0  Gene Names: 6, PBI_CHE8_6
UniProt
Find proteins for Q855K4 (Mycobacterium virus Che8) Explore Q855K4  Go to UniProtKB:  Q855K4

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.0
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	ISOLDE	1.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Podgorski, J.M., White, S.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-03-15
  Changes: Database references