9F04 | pdb_00009f04

Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 tail in the pre-contraction state - tube and sheath proteins

PDB DOI: https://doi.org/10.2210/pdb9F04/pdb
EM Map EMD-50093: EMDB EMDataResource

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

Deposited: 2024-04-15 Released: 2025-04-23
Deposition Author(s): Binovsky, J., Siborova, M., Skubnik, K., Novacek, J., Plevka, P.
Funding Organization(s): European Research Council (ERC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9F04

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

Literature

Cell attachment and tail contraction of S. aureus phage phi812

Binovsky, J., Siborova, M., Skubnik, K., Novacek, J., Plevka, P.

To be published.

Macromolecule Content

Total Structure Weight: 322.01 kDa
Atom Count: 20,968
Modeled Residue Count: 2,680
Deposited Residue Count: 2,916
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail sheath protein	A [auth G], B [auth F], C [auth H], D [auth E]	587	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A0A0U1WZ79 (Staphylococcus phage 812) Explore A0A0U1WZ79 Go to UniProtKB: A0A0U1WZ79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U1WZ79
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	E [auth D], F [auth C], G [auth B], H [auth A]	142	Staphylococcus phage 812	Mutation(s): 0
UniProt
Find proteins for A1YTP2 (Staphylococcus phage 812) Explore A1YTP2 Go to UniProtKB: A1YTP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1YTP2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101043452
Other government	Czech Republic	LX22NP05103

Revision History (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release
Version 1.1: 2025-07-09
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.