9WJR | pdb_00009wjr

Cryo-EM structure of the L. garvieae Man-PTS

• PDB DOI: https://doi.org/10.2210/pdb9WJR/pdb
• EM Map EMD-66027: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Lactococcus garvieae
• Expression System: Lactococcus phage phiL47
• Mutation(s): No 


• Deposited: 2025-08-31 Released: 2025-11-12 
• Deposition Author(s): Wang, J.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the broad-spectrum antimicrobial activity of Garvicin Q

Wang, J.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 200.43 kDa 
• Atom Count: 13,608 
• Modeled Residue Count: 1,821 
• Deposited Residue Count: 1,896 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose/fructose/sorbose family PTS transporter subunit IIC	A [auth Y], C [auth F], E [auth S]	267	Lactococcus garvieae	Mutation(s): 0  Gene Names: ptnC, ikelab_07180, OF801_03270, PWF74_01710, QHR29_06245, SAMN05216438_102202
UniProt
Find proteins for A0A1I4FTQ3 (Lactococcus garvieae) Explore A0A1I4FTQ3  Go to UniProtKB:  A0A1I4FTQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS mannose transporter subunit IID	B [auth Z], D [auth G], F [auth T]	365	Lactococcus garvieae	Mutation(s): 0  Gene Names: ptnD, ikelab_07170, OF801_03265, PWF74_01705, QHR29_06240
UniProt
Find proteins for A0A3D4RH01 (Lactococcus garvieae) Explore A0A3D4RH01  Go to UniProtKB:  A0A3D4RH01

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	G [auth Z], H [auth G], I [auth T]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Wang, J.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371254
National Natural Science Foundation of China (NSFC)	China	32171190

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release