8QGR | pdb_00008qgr

Stopper protein of phage 812 in closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.219 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.198 (DCC) 

Starting Model: in silico
View more details

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
Capsid proteinA [auth B]292Staphylococcus phage 812Mutation(s): 0 
Gene Names: 812_097812_099812a_099812F1_099K1/420_099K1_099
UniProt
Find proteins for A1YTN7 (Staphylococcus phage 812)
Explore A1YTN7 
Go to UniProtKB:  A1YTN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1YTN7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.219 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.366α = 90
b = 93.366β = 90
c = 122.531γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: Database references, Structure summary