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- PDB-9wjw: Cryo-EM structure of the GarQ-lmYZ complex -

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Basic information

Entry
Database: PDB / ID: 9wjw
TitleCryo-EM structure of the GarQ-lmYZ complex
Components
  • Mannose/fructose/sorbose family PTS transporter subunit IIC
  • PTS mannose family transporter subunit IID
  • Prepeptide GarQ
KeywordsMEMBRANE PROTEIN / antibiotic resistance / antimicrobial peptides / mannose phosphotransferase system / Man-PTS / bacteriocins / non-pediocin-like/class IId bacteriocins / Garvicin Q / GarQ
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / defense response to bacterium / extracellular region / plasma membrane
Similarity search - Function
Bacteriocin, class IId / Lactococcin-like family / Bacteriocin-type signal sequence / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile. / :
Similarity search - Domain/homology
alpha-D-mannopyranose / PTS mannose family transporter subunit IID / Prepeptide GarQ / Mannose/fructose/sorbose family PTS transporter subunit IIC
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Lactococcus garvieae (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWang, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: To Be Published
Title: Structural basis for the broad-spectrum antimicrobial activity of Garvicin Q
Authors: Wang, J.W.
History
DepositionAug 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Mannose/fructose/sorbose family PTS transporter subunit IIC
G: PTS mannose family transporter subunit IID
S: Mannose/fructose/sorbose family PTS transporter subunit IIC
T: PTS mannose family transporter subunit IID
A: Prepeptide GarQ
Y: Mannose/fructose/sorbose family PTS transporter subunit IIC
Z: PTS mannose family transporter subunit IID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,23010
Polymers187,6897
Non-polymers5403
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose/fructose/sorbose transporter subunit IIC / PTS system sorbose-specific EIIC component


Mass: 27377.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: S5LAD9
#2: Protein PTS mannose family transporter subunit IID / lmManZ / PTS mannose/fructose/sorbose transporter family subunit IID


Mass: 33402.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: E5H26_12035, FZW98_07125, GIH49_05195, IP987_000531 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E8EBU8
#3: Protein/peptide Prepeptide GarQ


Mass: 5349.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae (lactic acid bacteria)
Gene: garQ / Production host: Lactococcus phage phiL47 (virus) / References: UniProt: H6U5Y1
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Man-PTS from Lactococcus garvieae / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Lactococcus garvieae (lactic acid bacteria)1363
31Listeria monocytogenes (bacteria)1639
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Lactococcus phage phiL47 (virus)1412875
31Escherichia coli (E. coli)562
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55270 / Symmetry type: POINT
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312998
ELECTRON MICROSCOPYf_angle_d0.60517678
ELECTRON MICROSCOPYf_dihedral_angle_d4.421790
ELECTRON MICROSCOPYf_chiral_restr0.042131
ELECTRON MICROSCOPYf_plane_restr0.0052172

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