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- EMDB-63072: Cryo-EM structure of the glucose-specific PTS transporter IIC fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-63072
TitleCryo-EM structure of the glucose-specific PTS transporter IIC from V. cholerae in the inward-facing conformation
Map data
Sample
  • Complex: PTS system glucose-specific EIIC component
    • Protein or peptide: PTS system glucose-specific EIICB component
KeywordsPTS transporter / cryo-em / V. cholerae / TRANSPORT PROTEIN
Function / homology
Function and homology information


protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / plasma membrane
Similarity search - Function
PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. ...PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC
Similarity search - Domain/homology
PTS system glucose-specific EIICB component
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (strain M66-2) (bacteria) / Vibrio cholerae M66-2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsGuo HH / Zhang QS / Wang Z / Zhang K / Fu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the glucose-specific PTS transporter IIC from V. cholerae in the inward-facing conformation
Authors: Guo HH
History
DepositionJan 10, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63072.png

Downloads & links

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Map

FileDownload / File: emd_63072.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 360 pix.
= 240.48 Å		0.67 Å/pix.
x 360 pix.
= 240.48 Å		0.67 Å/pix.
x 360 pix.
= 240.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.029303513 - 2.1878688
Average (Standard dev.)0.0011637151 (±0.022052433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 240.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63072_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_63072_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 : PTS system glucose-specific EIIC component

EntireName: PTS system glucose-specific EIIC component
Components
  • Complex: PTS system glucose-specific EIIC component
    • Protein or peptide: PTS system glucose-specific EIICB component

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Supramolecule #1: PTS system glucose-specific EIIC component

SupramoleculeName: PTS system glucose-specific EIIC component / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae serotype O1 (strain M66-2) (bacteria)

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Macromolecule #1: PTS system glucose-specific EIICB component

MacromoleculeName: PTS system glucose-specific EIICB component / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: protein-Npi-phosphohistidine-D-glucose phosphotransferase
Source (natural)Organism: Vibrio cholerae M66-2 (bacteria)
Molecular weightTheoretical: 39.997566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AFANLQKVGK ALMLPVSVLP VAGILLGVGA ANFSWLPEVV SHLMEQAGGS VFGQMPLLFA VGVALGFTNN DGVSGLSAIV GYGIMVATL KVMATVMGVS GIDTGVLGGI LAGGVAAWSF NRFYKIQLPE YLGFFAGKRA VPIITGFISI ALGVVLSFIW P PIGSAIAT ...String:
AFANLQKVGK ALMLPVSVLP VAGILLGVGA ANFSWLPEVV SHLMEQAGGS VFGQMPLLFA VGVALGFTNN DGVSGLSAIV GYGIMVATL KVMATVMGVS GIDTGVLGGI LAGGVAAWSF NRFYKIQLPE YLGFFAGKRA VPIITGFISI ALGVVLSFIW P PIGSAIAT FSDWAANQDP VTAFGIYGIV ERSLIPFGLH HIWNVPFFYQ AGTCVNGAGE TVNGIMTCFL TADDASRAAG NG FGQLAGG YLFKMFGLPA AAFAIAHCAK PENRAKVMGI MASAALTSFL TGITEPIEFA FLFVAPVLYA IHAVLAGLAY VLT NALGVV HGHTFSNGFI DFVVQSPRAD NMLLLVGLGI GYAVLYYVVF TFVIRALNLK TPGRED

UniProtKB: PTS system glucose-specific EIICB component

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87760
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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