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- PDB-9wjr: Cryo-EM structure of the L. garvieae Man-PTS -

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Basic information

Entry
Database: PDB / ID: 9wjr
TitleCryo-EM structure of the L. garvieae Man-PTS
Components
  • Mannose/fructose/sorbose family PTS transporter subunit IIC
  • PTS mannose transporter subunit IID
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 / plasma membrane
Similarity search - Function
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 / Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose transporter subunit IID
Similarity search - Component
Biological speciesLactococcus garvieae (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 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
Y: Mannose/fructose/sorbose family PTS transporter subunit IIC
Z: PTS mannose transporter subunit IID
F: Mannose/fructose/sorbose family PTS transporter subunit IIC
G: PTS mannose transporter subunit IID
S: Mannose/fructose/sorbose family PTS transporter subunit IIC
T: PTS mannose transporter subunit IID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,4339
Polymers199,8926
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 / lgManY / PTS mannose/fructose/sorbose transporter subunit IIC / PTS system / mannose-specific IIC component


Mass: 27177.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae (lactic acid bacteria)
Gene: ptnC, ikelab_07180, OF801_03270, PWF74_01710, QHR29_06245, SAMN05216438_102202
Production host: Lactococcus phage phiL47 (virus) / References: UniProt: A0A1I4FTQ3
#2: Protein PTS mannose transporter subunit IID / lgManZ / PTS system mannose/fructose/sorbose family transporter subunit IID


Mass: 39453.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae (lactic acid bacteria)
Gene: ptnD, ikelab_07170, OF801_03265, PWF74_01705, QHR29_06240
Production host: Lactococcus phage phiL47 (virus) / References: UniProt: A0A3D4RH01
#3: 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-#2 / Source: RECOMBINANT
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)
Source (recombinant)Organism: Lactococcus phage phiL47 (virus)
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: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 876434 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313911
ELECTRON MICROSCOPYf_angle_d0.55718954
ELECTRON MICROSCOPYf_dihedral_angle_d4.0961911
ELECTRON MICROSCOPYf_chiral_restr0.042271
ELECTRON MICROSCOPYf_plane_restr0.0062349

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