7X30

Capsid structure of Staphylococcus jumbo bacteriophage S6

• PDB DOI: https://doi.org/10.2210/pdb7X30/pdb
• EM Map EMD-32974: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Staphylococcus phage S6
• Mutation(s): No 


• Deposited: 2022-02-27 Released: 2023-12-06 
• Deposition Author(s): Koibuchi, W., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Capsid structure of Staphylococcus jumbo bacteriophage S6

Koibuchi, W., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 1860-mer - A1620B240 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,812.6 kDa 
• Atom Count: 105,389 
• Modelled Residue Count: 13,432 
• Deposited Residue Count: 16,322 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major structural protein ORF12	A, AA [auth z], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e], G [auth f], H [auth g], I [auth h], J [auth i], K [auth j], L [auth k], M [auth l], N [auth m], O [auth n], P [auth o], Q [auth p], R [auth q], S [auth r], T [auth s], U [auth t], V [auth u], W [auth v], X [auth w], Y [auth x], Z [auth y]	534	Staphylococcus phage S6	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hoc-like protein ORF90	BA [auth P], CA [auth Q], DA [auth R], EA [auth S]	476	Staphylococcus phage S6	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Koibuchi, W., Uchiyama, J., Matsuzaki, S., Murata, K., Iwasaki, K., Miyazaki, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K18521
Japan Society for the Promotion of Science (JSPS)	Japan	18K06154

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release