9F04 | pdb_00009f04

Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 tail in the pre-contraction state - tube and sheath proteins

• PDB DOI: https://doi.org/10.2210/pdb9F04/pdb
• EM Map EMD-50093: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Staphylococcus phage 812
• Mutation(s): No 


• Deposited: 2024-04-15 Released: 2025-04-23 
• Deposition Author(s): Binovsky, J., Siborova, M., Skubnik, K., Novacek, J., Plevka, P.
• Funding Organization(s): European Research Council (ERC), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cell attachment and tail contraction of S. aureus phage phi812

Binovsky, J., Siborova, M., Skubnik, K., Novacek, J., Plevka, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A24B24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 322.01 kDa 
• Atom Count: 20,968 
• Modeled Residue Count: 2,680 
• Deposited Residue Count: 2,916 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail sheath protein	A [auth G], B [auth F], C [auth H], D [auth E]	587	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WZ79 (Staphylococcus phage 812) Explore A0A0U1WZ79  Go to UniProtKB:  A0A0U1WZ79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	E [auth D], F [auth C], G [auth B], H [auth A]	142	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTP2 (Staphylococcus phage 812) Explore A1YTP2  Go to UniProtKB:  A1YTP2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Binovsky, J., Siborova, M., Skubnik, K., Novacek, J., Plevka, P.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101043452
Other government	Czech Republic	LX22NP05103

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Data collection