8QEM | pdb_00008qem

Neck channel of phage 812 after tail contraction (C1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Genome anchoring, retention, and release by neck proteins of Staphylococcus phage 812.

Cienikova, Z.Novacek, J.Siborova, M.Popelarova, B.Fuzik, T.Botka, T.Benesik, M.Bardy, P.Pantucek, R.Plevka, P.

(2026) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-025-09477-8
  • Primary Citation of Related Structures:  
    8Q01, 8Q1I, 8Q7D, 8QEK, 8QEM, 8QGR, 8QJE, 8QKH, 8R5G, 8R69

  • PubMed Abstract: 

    The virion of Staphylococcus phage 812 is formed by a capsid and a contractile tail joined together by neck proteins. The neck proteins are crucial for virion assembly, DNA packaging, and the regulation of genome release, but their functions are not completely understood. Here, we show that the neck of phage 812 consists of portal, adaptor, stopper, tail terminator, and two types of decoration proteins. A dodecameric DNA-binding site at the surface of the portal complex anchors the phage genome inside the capsid. The adaptor complex induces a local B-to-A form transition of the DNA in the neck channel that could slow or pause genome translocation during ejection. The central channel of a stopper complex that is not attached to the tail terminator complex is closed by gating loops. In contrast, in the phage 812 virion, the gating loops are in an open conformation, and the DNA extends into the tail. The structure of neck proteins is not affected by tail sheath contraction. Therefore, the expulsion of tail tape measure proteins triggers the genome release.


  • Organizational Affiliation
    • CEITEC Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative neck protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
302Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A1YTN6 (Staphylococcus phage 812)
Explore A1YTN6 
Go to UniProtKB:  A1YTN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1YTN6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
563Staphylococcus phage 812Mutation(s): 0 
UniProt
Find proteins for A0A0U1WIV9 (Staphylococcus phage 812)
Explore A0A0U1WIV9 
Go to UniProtKB:  A0A0U1WIV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1WIV9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Channel DNA reverse strand (63-MER)Y [auth Z]63Staphylococcus phage 812
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Channel DNA forward strand (63-MER)Z [auth Y]63Staphylococcus phage 812
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech Republic--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references, Structure summary