9YGB | pdb_00009ygb

CryoEM structure of F7 pyocin tail tip in the pre-ejection state

• PDB DOI: https://doi.org/10.2210/pdb9YGB/pdb
• EM Map EMD-72919: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 2025-09-28 Released: 2026-09-30 
• Deposition Author(s): He, Y., Cai, X.Y., Li, A.S.C., Davidson, A.R., Zhou, Z.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atomic structures and bactericidal actions of a non-contractile tailocin against Pseudomonas aeruginosa

He, Y., Cai, X.Y., Li, A.S.C., Davidson, A.R., Zhou, Z.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A6B6C3D3E3F3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 892.39 kDa 
• Atom Count: 39,159 
• Modeled Residue Count: 5,088 
• Deposited Residue Count: 8,277 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail tape measure protein	A [auth F], I [auth S], Q [auth T]	612	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0A643J2J4 (Pseudomonas aeruginosa) Explore A0A643J2J4  Go to UniProtKB:  A0A643J2J4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail protein	B [auth H], D [auth G], J [auth W], L [auth U], R [auth X], T [auth V]	164	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q9R3G3 (Pseudomonas aeruginosa) Explore Q9R3G3  Go to UniProtKB:  Q9R3G3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MF2 protein	C, G [auth D], K [auth M], O, S [auth N], W [auth P]	113	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q9S561 (Pseudomonas aeruginosa) Explore Q9S561  Go to UniProtKB:  Q9S561

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phage tail assembly protein	E, M [auth Q], U [auth R]	200	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0A0H2ZLF4 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZLF4  Go to UniProtKB:  A0A0H2ZLF4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail protein	F [auth A], N [auth I], V [auth J]	1,162	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0A7M2ZXW7 (Pseudomonas aeruginosa) Explore A0A7M2ZXW7  Go to UniProtKB:  A0A7M2ZXW7

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail hub protein of F7 pyocin	H [auth B], P [auth K], X [auth L]	231	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0A3E1N7Q2 (Pseudomonas aeruginosa) Explore A0A3E1N7Q2  Go to UniProtKB:  A0A3E1N7Q2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	AA [auth L], Y [auth B], Z [auth K]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): He, Y., Cai, X.Y., Li, A.S.C., Davidson, A.R., Zhou, Z.H.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI094386

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release