7CLR

CryoEM structure of S.typhimurium flagellar LP ring

• PDB DOI: https://doi.org/10.2210/pdb7CLR/pdb
• EM Map EMD-30398: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-07-21 Released: 2021-06-02 
• Deposition Author(s): Yamaguchi, T., Makino, F., Miyata, T., Minamino, T., Kato, T., Namba, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the molecular bushing of the bacterial flagellar motor.

Yamaguchi, T., Makino, F., Miyata, T., Minamino, T., Kato, T., Namba, K.

(2021) Nat Commun 12: 4469-4469

• PubMed: 34294704 
• DOI: https://doi.org/10.1038/s41467-021-24715-3
• Primary Citation of Related Structures:  
  7CLR


• PubMed Abstract: 
  

  The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface.

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Organizational Affiliation: 

Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C26  (Explore in 3D)
Global Stoichiometry: Hetero 52-mer - A26B26 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: scanning transmission electron microscopy

Macromolecule Content

• Total Structure Weight: 1,635.94 kDa 
• Atom Count: 98,878 
• Modelled Residue Count: 13,338 
• Deposited Residue Count: 15,522 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar P-ring protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	365	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P15930 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P15930  Go to UniProtKB:  P15930

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar L-ring protein	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	232	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A1N8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1N8  Go to UniProtKB:  P0A1N8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13
MODEL REFINEMENT	Coot	0.8.9.1
RECONSTRUCTION	RELION	3.0 beta-2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Yamaguchi, T., Makino, F., Miyata, T., Minamino, T., Kato, T., Namba, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP25000013,JP18K06155,JP26293097,JP19H03182,JP15H01640
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101117,JP17pc0101020

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2021-06-09
  Changes: Database references
• Version 1.2: 2021-12-22
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary