9EFK | pdb_00009efk

Cryo-EM structure of the portal-tail complex of LME-1 phage

• PDB DOI: https://doi.org/10.2210/pdb9EFK/pdb
• EM Map EMD-47975: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Legionella pneumophila
• Mutation(s): No 


• Deposited: 2024-11-20 Released: 2025-04-16 
• Deposition Author(s): Deme, J.C., Lea, S.M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Phage resistance as an unexpected environmental determinant of the accidental virulence of Legionella pneumophila against the human host.

Nicholson, B., Sante, J.F., Chaney, E.H., Deme, J.C., Deecker, S.R., Sztanko, K., Davidson, A.R., Lea, S.M., Ensminger, A.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A18B12C12D6 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,804.71 kDa 
• Atom Count: 129,576 
• Modeled Residue Count: 16,542 
• Deposited Residue Count: 25,812 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
orf12	A, AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], Z [auth B]	554	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYN0 (Legionella pneumophila) Explore A0A140AYN0  Go to UniProtKB:  A0A140AYN0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
orf18	B [auth M], C [auth N], D [auth O], E [auth P], F [auth Q], G [auth R]	818	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYN6 (Legionella pneumophila) Explore A0A140AYN6  Go to UniProtKB:  A0A140AYN6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
orf22	H [auth AE], I [auth AF], J [auth AG], K [auth AN], L [auth AO], M [auth AP], N [auth AW], O [auth AX], P [auth AY], Q [auth BF], R [auth BG], S [auth BH], T [auth BO], U [auth BP], V [auth BQ], W [auth BX], X [auth BY], Y [auth BZ]	658	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYP0 (Legionella pneumophila) Explore A0A140AYP0  Go to UniProtKB:  A0A140AYP0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
orf17	KA [auth T], LA [auth AC], MA [auth AD], NA [auth S], OA [auth X], PA [auth U], QA [auth V], RA [auth W], SA [auth Y], TA [auth Z], UA [auth AA], VA [auth AB]	201	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYN5 (Legionella pneumophila) Explore A0A140AYN5  Go to UniProtKB:  A0A140AYN5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5430

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Deme, J.C., Lea, S.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release