9WJW | pdb_00009wjw

Cryo-EM structure of the GarQ-lmYZ complex

• PDB DOI: https://doi.org/10.2210/pdb9WJW/pdb
• EM Map EMD-66032: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Listeria monocytogenes, Lactococcus garvieae
• Expression System: Escherichia coli, 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: 2.96 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: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B3C1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 188.23 kDa 
• Atom Count: 12,735 
• Modeled Residue Count: 1,689 
• Deposited Residue Count: 1,763 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose/fructose/sorbose family PTS transporter subunit IIC	A [auth F], C [auth S], F [auth Y]	268	Listeria monocytogenes	Mutation(s): 0  Gene Names:  sorA, sora, A3R20_11195, A8L61_14515, AB917_01950, ABZ57_09825, AE233_00630, AJL21_02165, AP104_04065, ARR48_10220, ART25_13030, ARY78_13630, B1N52_06240, B1S26_07815, B4X68_12445, B5K54_07660, BB997_05725, BCZ19_15275, BCZ21_05325, CA369_04850, CAC64_07455, CAV64_13735, CW845_05135, CW895_08900, D4920_07280, D4B11_07875, D5N24_06625, D7104_05030, DCK61_14375, DCT16_05775, DQ70_12490, DU018_08255, DYZ80_00883, E1W56_07855, E1X78_07945, E5F58_14000, E5H26_12030, EX365_09020, EXZ73_03360, F6436_01900, F6515_08315, FA835_09550, FLQ97_00880, FLR03_08660, FNX40_02200, FV747_01955, FZW98_07120, G3O21_000383, GHH22_13960, GI949_01920, GIH49_05190, GJW51_04690, GQG13_06195, GYR60_10730, GYS09_07230, GYX23_01860, GYY14_04735, HQN34_001832, HZJ64_04955, IP987_000532, KV70_01895, QD52_06040, UI29_06055, Y261_12645
UniProt
Find proteins for S5LAD9 (Listeria monocytogenes) Explore S5LAD9  Go to UniProtKB:  S5LAD9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS mannose family transporter subunit IID	B [auth G], D [auth T], G [auth Z]	303	Listeria monocytogenes	Mutation(s): 0  Gene Names: E5H26_12035, FZW98_07125, GIH49_05195, IP987_000531
UniProt
Find proteins for A0A1E8EBU8 (Listeria monocytogenes) Explore A0A1E8EBU8  Go to UniProtKB:  A0A1E8EBU8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Prepeptide GarQ	E [auth A]	50	Lactococcus garvieae	Mutation(s): 0  Gene Names: garQ
UniProt
Find proteins for H6U5Y1 (Lactococcus garvieae) Explore H6U5Y1  Go to UniProtKB:  H6U5Y1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.96 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