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 9EUF | pdb_00009euf

Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the pre-contraction state - complete


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history. 

Literature

Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.

Binovsky, J., Siborova, M., Zlatohurska, M., Novacek, J., Bardy, P., Baska, R., Skubnik, K., Botka, T., Benesik, M., Pantucek, R., Tripsianes, K., Plevka, P.

(2026) EMBO J 45: 5514-5536

  • DOI: https://doi.org/10.1038/s44318-026-00834-9
  • Primary Citation Related Structures: 
    9EUF, 9EUI, 9EUJ, 9EUK, 9EUL, 9EUM, 9F04, 9F05, 9F06, 9FKO, 9TIC, 9TID, 9TIE, 9TIF, 9TIG, 9TIH, 9TII, 9TIJ, 9TIK, 9TIL, 9TIM, 9TIN, 9TIO, 9TIP, 9TIR, 9TIS, 9TIT, 9TIW

  • PubMed Abstract: 

    Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.


  • Organizational Affiliation: 
    • Central European Institute of Technology, Brno, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 3,795.97 kDa 
  • Atom Count: 160,477 
  • Modeled Residue Count: 30,231 
  • Deposited Residue Count: 33,837 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF4815 domain-containing protein1,152Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0H4TGK5 (Staphylococcus phage IME-SA119)
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UniProt GroupA0A0H4TGK5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor binding protein458Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WIJ9 (Staphylococcus phage 812)
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Entity Groups
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UniProt GroupA0A0U1WIJ9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CBM-cenC domain-containing protein640Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1UXW5 (Staphylococcus phage 812)
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UniProt GroupA0A0U1UXW5
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NlpC/P60 domain-containing proteinK [auth A]295Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1UXW0 (Staphylococcus phage 812)
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Entity Groups
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UniProt GroupA0A0U1UXW0
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
GP-PDE domain-containing proteinM [auth B]848Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WFD7 (Staphylococcus phage 812)
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UniProt GroupA0A0U1WFD7
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate componentN [auth C],
O [auth D],
T [auth I],
V [auth K]
348Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WF63 (Staphylococcus phage 812)
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UniProt GroupA0A0U1WF63
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidase C51 domain-containing proteinP [auth E]808Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1X189 (Staphylococcus phage 812)
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UniProt GroupA0A0U1X189
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate componentQ [auth F],
R [auth G]
174Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1UXD6 (Staphylococcus phage 812)
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UniProt GroupA0A0U1UXD6
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
TmpFS [auth H],
U [auth J]
1,019Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WGD3 (Staphylococcus phage 812)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate wedge subunitW [auth L],
Z [auth O]
234Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1UXD7 (Staphylococcus phage 812)
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UniProt GroupA0A0U1UXD7
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative baseplate componentX [auth M],
Y [auth N]
263Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1X2L4 (Staphylococcus phage 812)
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UniProt GroupA0A0U1X2L4
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Major tail sheath protein587Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WZ79 (Staphylococcus phage 812)
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UniProt GroupA0A0U1WZ79
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein142Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A1YTP2 (Staphylococcus phage 812)
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UniProt GroupA1YTP2
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate protein194Staphylococcus phage 812Mutation(s): 0 
Gene Names: 812_119, 812_121, 812a_121, 812F1_121, K1/420_121, K1_121
UniProt
Find proteins for A0A0U1WGQ5 (Staphylococcus phage 812)
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UniProt GroupA0A0U1WGQ5
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101043452
Other governmentCzech RepublicLX22NP05103

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2026-10-21
    Changes: Data collection, Database references