9EG4 | pdb_00009eg4

Cryo-EM structure of the icosahedral capsid of LME-1 phage

PDB DOI: https://doi.org/10.2210/pdb9EG4/pdb
EM Map EMD-47984: EMDB EMDataResource

Classification: VIRUS
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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

Total Structure Weight: 413.25 kDa
Atom Count: 20,202
Modeled Residue Count: 2,639
Deposited Residue Count: 3,906
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage major capsid protein	A E [auth C] F [auth E] J [auth D] K [auth F] A, E [auth C], F [auth E], J [auth D], K [auth F], L [auth B], M [auth G]	289	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYN3 (Legionella pneumophila) Explore A0A140AYN3 Go to UniProtKB: A0A140AYN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140AYN3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
orf16	B [auth H] C [auth I] D [auth J] G [auth K] H [auth L] B [auth H], C [auth I], D [auth J], G [auth K], H [auth L], I [auth M], N	269	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for A0A140AYN4 (Legionella pneumophila) Explore A0A140AYN4 Go to UniProtKB: A0A140AYN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A140AYN4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-04-16
Type: Initial release
Version 1.1: 2025-05-28
Changes: Data collection

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.