9U82 | pdb_00009u82

Cryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose

• PDB DOI: https://doi.org/10.2210/pdb9U82/pdb
• EM Map EMD-63950: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Leminorella grimontii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-25 Released: 2025-10-15 
• Deposition Author(s): Takahashi, Y.S., Kohga, H., Shigematsu, H., Miyazaki, R., Tsukazaki, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of a GatC ortholog transporter in the bacterial phosphotransferase system.

Takahashi, Y.S., Kohga, H., Chek, M.F., Yamamoto, K., Takahashi, J.F., Shigematsu, H., Tanaka, Y., Ichikawa, M., Miyazaki, R., Hakoshima, T., Tsukazaki, T.

(2025) FEBS Lett 599: 2377-2387

• PubMed: 40878824 
• DOI: https://doi.org/10.1002/1873-3468.70135
• Primary Citation of Related Structures:  
  9U82, 9U84, 9U8E, 9U8H


• PubMed Abstract: 
  

  The bacterial phosphotransferase system (PTS) mediates the uptake of specific carbohydrates via IIC transporters. Here, we report the crystal and cryo-electron microscopy (cryo-EM) structures of Leminorella grimontii galactitol-specific PTS enzyme IIC component (LgGatC), which is implicated in D-xylose uptake and belongs to the ascorbate-galactitol (AG) superfamily of IIC proteins. These structures, determined in the presence and absence of D-xylose, capture the transporter in an outward-facing conformation. A homology model of an inward-facing state, constructed based on these structures, supports an elevator-like transport mechanism. These findings provide structural insights into substrate recognition by GatC and offer a framework for understanding sugar transport in PTS IIC proteins.

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Organizational Affiliation: 
• Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan.
Institute for Research Initiatives, Nara Institute of Science and Technology, Japan.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan.
School of Life Sciences, Fudan University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 100.16 kDa 
• Atom Count: 6,708 
• Modeled Residue Count: 896 
• Deposited Residue Count: 942 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS galactitol transporter subunit IIC	A, B	471	Leminorella grimontii	Mutation(s): 0  Gene Names: SOASR030_34840
UniProt
Find proteins for A0AAV5N9B3 (Leminorella grimontii) Explore A0AAV5N9B3  Go to UniProtKB:  A0AAV5N9B3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Takahashi, Y.S., Kohga, H., Shigematsu, H., Miyazaki, R., Tsukazaki, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Data collection, Database references