8Q7D

Neck of phage 812 after tail contraction (C12)

• PDB DOI: https://doi.org/10.2210/pdb8Q7D/pdb
• EM Map EMD-18213: EMDB EMDataResource
• NAKB: 8Q7D

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


• Deposited: 2023-08-16 Released: 2024-08-28 
• Deposition Author(s): Cienikova, Z., Siborova, M., Fuzik, T., Plevka, P.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.07 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 172.45 kDa 
• Atom Count: 10,571 
• Modelled Residue Count: 940 
• Deposited Residue Count: 1,105 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative neck protein	A [auth d]	302	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTN6 (Staphylococcus phage 812) Explore A1YTN6  Go to UniProtKB:  A1YTN6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	B [auth p]	563	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WIV9 (Staphylococcus phage 812) Explore A0A0U1WIV9  Go to UniProtKB:  A0A0U1WIV9

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA forward strand (120-MER)	C [auth Y]	120	Staphylococcus phage 812

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA reverse strand (120-MER)	D [auth Z]	120	Staphylococcus phage 812

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.07 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19
MODEL REFINEMENT	ISOLDE	1.4
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Cienikova, Z., Siborova, M., Fuzik, T., Plevka, P.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release