9E99 | pdb_00009e99

Cryo-EM reconstruction of Escherichia phage N4 capsid

• PDB DOI: https://doi.org/10.2210/pdb9E99/pdb
• EM Map EMD-47777: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage N4
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-11-07 Released: 2025-02-19 
• Deposition Author(s): Eruera, A., McJarrow-Keller, K., Hyun, J.K., Bostina, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atlas of Interactions Between Decoration Proteins and Major Capsid Proteins of Coliphage N4.

McJarrow-Keller, K., Eruera, A.R., Crowe, A.J.M., Kumaran, R., Hyun, J., Bostina, M.

(2024) Viruses 17

• PubMed: 39861808 
• DOI: https://doi.org/10.3390/v17010019
• Primary Citation of Related Structures:  
  9E99


• PubMed Abstract: 
  

  Coliphage N4 is a representative species of the Schitoviridae family of bacteriophages. Originally structurally studied in 2008, the capsid structure was solved to 14 Å to reveal an interesting arrangement of Ig-like decoration proteins across the surface of the capsid. Herein, we present a high-resolution N4 structure, reporting a 2.45 Å map of the capsid obtained via single particle cryogenic-electron microscopy. Structural analysis of the major capsid proteins (MCPs) and decoration proteins (gp56 and gp17) of phage N4 reveals a pattern of interactions across the capsid that are mediated by structurally homologous domains of gp17. In this study, an analysis of the complex interface contacts allows us to confirm that the gp17 Ig-like decoration proteins of N4 are likely employed by the virus to increase the capsid's structural integrity.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.
School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A9B3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A4B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 484.29 kDa 
• Atom Count: 33,875 
• Modeled Residue Count: 4,436 
• Deposited Residue Count: 4,446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D, E, F, G, H, I	401	Escherichia phage N4	Mutation(s): 0  Gene Names: 56
UniProt
Find proteins for Q859Q5 (Enterobacteria phage N4) Explore Q859Q5  Go to UniProtKB:  Q859Q5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
32 kDa protein	J, K, L	279	Escherichia phage N4	Mutation(s): 0
UniProt
Find proteins for A0MZA7 (Enterobacteria phage N4) Explore A0MZA7  Go to UniProtKB:  A0MZA7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Eruera, A., McJarrow-Keller, K., Hyun, J.K., Bostina, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release