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- EMDB-66030: Cryo-EM structure of the L. garvieae Man-PTS in complex with the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66030
TitleCryo-EM structure of the L. garvieae Man-PTS in complex with the bacteriocin GarQ
Map data
Sample
  • Complex: Man-PTS from Lactococcus garvieae
    • Protein or peptide: Prepeptide GarQ
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose transporter subunit IID
  • Ligand: alpha-D-mannopyranose
Keywordsantibiotic resistance / antimicrobial peptides / mannose phosphotransferase system / Man-PTS / bacteriocins / non-pediocin-like/class IId bacteriocins / Garvicin Q / GarQ / MEMBRANE PROTEIN
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
Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose transporter subunit IID / Prepeptide GarQ
Similarity search - Component
Biological speciesLactococcus garvieae (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsWang JW
Funding support China, 2 items
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 JW
History
DepositionAug 31, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66030.png

Downloads & links

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Map

FileDownload / File: emd_66030.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 272 pix.
= 292.182 Å		1.07 Å/pix.
x 272 pix.
= 292.182 Å		1.07 Å/pix.
x 272 pix.
= 292.182 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.9812262 - 1.7054596
Average (Standard dev.)-0.000011666924 (±0.05379368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 292.1824 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66030_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66030_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Man-PTS from Lactococcus garvieae

EntireName: Man-PTS from Lactococcus garvieae
Components
  • Complex: Man-PTS from Lactococcus garvieae
    • Protein or peptide: Prepeptide GarQ
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose transporter subunit IID
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Man-PTS from Lactococcus garvieae

SupramoleculeName: Man-PTS from Lactococcus garvieae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)

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Macromolecule #1: Mannose/fructose/sorbose family PTS transporter subunit IIC

MacromoleculeName: Mannose/fructose/sorbose family PTS transporter subunit IIC
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)
Molecular weightTheoretical: 27.177129 KDa
Recombinant expressionOrganism: Lactococcus phage phiL47 (virus)
SequenceString: MSIISIILVL IFAFLAGLEG ILDQWQFHQP IIACSLIGIA TGHMAAGIIL GGSLQMIALG WANVGAAVAP DAALASVASA ILMVQGGNF DLTHITGVIV PAAILLATAG LVLTTLVRFL SVGIVHLADA AAEKGSYSGV AGWHMFALLL QGLRIAIPAA I ILAIPAET ...String:
MSIISIILVL IFAFLAGLEG ILDQWQFHQP IIACSLIGIA TGHMAAGIIL GGSLQMIALG WANVGAAVAP DAALASVASA ILMVQGGNF DLTHITGVIV PAAILLATAG LVLTTLVRFL SVGIVHLADA AAEKGSYSGV AGWHMFALLL QGLRIAIPAA I ILAIPAET VTAALNAIPD WVSKGLAVGG GMVVVVGYAM VINLMATKEL WPFFFLGFVL APLSSITLIG MGILGVVIAL IY LNLSNTA GNGGTASSSG DPIGDILNDY

UniProtKB: Mannose/fructose/sorbose family PTS transporter subunit IIC

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Macromolecule #2: PTS mannose transporter subunit IID

MacromoleculeName: PTS mannose transporter subunit IID / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)
Molecular weightTheoretical: 39.453551 KDa
Recombinant expressionOrganism: Lactococcus phage phiL47 (virus)
SequenceString: MENTNKKFSL SKNTRLSVMF RSMFLQGSWN YERMQNLGFL YSIIPALKQF YKPGSEEAKE ALKRHMEFFN THPYVAAPIV GVTLALEEE IANGVEIDEA AIQGVKVGMM GPLAGIGDPV FWFTVRPIVG AIAASLATGG SIIAPIFFFV VWNAIRIAFL W YTQEFGYK ...String:
MENTNKKFSL SKNTRLSVMF RSMFLQGSWN YERMQNLGFL YSIIPALKQF YKPGSEEAKE ALKRHMEFFN THPYVAAPIV GVTLALEEE IANGVEIDEA AIQGVKVGMM GPLAGIGDPV FWFTVRPIVG AIAASLATGG SIIAPIFFFV VWNAIRIAFL W YTQEFGYK QGTAITSDLG GGMLQQITKG ASILGMFILG VLIQRWVNIS FTGPNAMLPS KPLADGAYVG EWIDKAGKVV VQ GAQTGTT GDGVAKFDWL DQAGNGVGNG VAGQGGFAHY VTVDQLNTVD GSTLHNILGQ VSSGLGLSPE QTQSLQDVFN SLI PGFIAL LLTFLVLWIL RKWKNKNAPL FIIIGMFVLG IVLHVAGLA

UniProtKB: PTS mannose transporter subunit IID

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Macromolecule #3: Prepeptide GarQ

MacromoleculeName: Prepeptide GarQ / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus garvieae (lactic acid bacteria)
Molecular weightTheoretical: 5.488098 KDa
Recombinant expressionOrganism: Lactococcus phage phiL47 (virus)
SequenceString:
HEYHLMNGAN GYLTRVNGKY VYRVTKDPVS AVFGVISNGW GSAGAGFGPQ H

UniProtKB: Prepeptide GarQ

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Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 114159
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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