8R5G

Neck-tail junction of phage 812 virion (C6)

• PDB DOI: https://doi.org/10.2210/pdb8R5G/pdb
• EM Map EMD-18912: EMDB EMDataResource

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


• Deposited: 2023-11-16 Released: 2024-11-27 
• Deposition Author(s): Cienikova, Z., Novacek, J., Fuzik, T., Benesik, M., 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: 4.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: 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., Pantucek, R., Plevka, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 72-mer - A12B12C12D12E12F6G6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 351.07 kDa 
• Atom Count: 23,334 
• Modelled Residue Count: 2,927 
• Deposited Residue Count: 3,110 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	292	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTN7 (Staphylococcus phage 812) Explore A1YTN7  Go to UniProtKB:  A1YTN7

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate hub assembly protein	C [auth G]	278	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTN9 (Staphylococcus phage 812) Explore A1YTN9  Go to UniProtKB:  A1YTN9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative non-cytoplasmic protein	D [auth M], J [auth W]	87	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WZ69 (Staphylococcus phage 812) Explore A0A0U1WZ69  Go to UniProtKB:  A0A0U1WZ69

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail sheath protein	E [auth N], K [auth V]	587	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WZ79 (Staphylococcus phage 812) Explore A0A0U1WZ79  Go to UniProtKB:  A0A0U1WZ79

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-cytoplasmic protein	F [auth S], L [auth U]	152	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WIM1 (Staphylococcus phage 812) Explore A0A0U1WIM1  Go to UniProtKB:  A0A0U1WIM1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative neck protein	G [auth Z], H [auth Y]	302	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTN6 (Staphylococcus phage 812) Explore A1YTN6  Go to UniProtKB:  A1YTN6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.28 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: 2024-11-27 
Deposition Author(s): Cienikova, Z., Novacek, J., Fuzik, T., Benesik, M., 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: 2024-11-27
  Type: Initial release