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- EMDB-66479: Gut transporter with sorbitol -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66479
TitleGut transporter with sorbitol
Map data
Sample
  • Complex: Gut transporter with sorbitol
    • Protein or peptide: PTS system glucitol/sorbitol-specific EIIB component
    • Protein or peptide: PTS system glucitol/sorbitol-specific EIIC component
  • Ligand: sorbitol
Keywordssugar phosphotransferase system / PTS / glucitol/sorbitol / PTS Gut family / TRANSPORT PROTEIN
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-sorbitol phosphotransferase / sorbitol transmembrane transport / protein-phosphocysteine-sugar phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / plasma membrane
Similarity search - Function
Phosphotransferase system, enzyme II sorbitol-specific factor / Phosphotransferease, sorbitol phosphotransferase enzyme II / Sorbitol phosphotransferase enzyme II, N-terminal / Sorbitol phosphotransferase enzyme II, C-terminal / PTS system enzyme II sorbitol-specific factor / Sorbitol phosphotransferase enzyme II N-terminus / Sorbitol phosphotransferase enzyme II C-terminus / PTS_EIIB type-5 domain profile. / PTS_EIIC type-5 domain profile.
Similarity search - Domain/homology
PTS system glucitol/sorbitol-specific EIIC component / PTS system glucitol/sorbitol-specific EIIB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsDeng T / Ge X / Wang J
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
National Natural Science Foundation of China (NSFC)32501078 China
CitationJournal: To Be Published
Title: Gut transporter with sorbitol
Authors: Deng T / Ge X / Wang J
History
DepositionOct 6, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66479.png

Downloads & links

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Map

FileDownload / File: emd_66479.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å		0.96 Å/pix.
x 320 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.3449802 - 4.538481
Average (Standard dev.)0.004198278 (±0.090367205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 307.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66479_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_66479_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 : Gut transporter with sorbitol

EntireName: Gut transporter with sorbitol
Components
  • Complex: Gut transporter with sorbitol
    • Protein or peptide: PTS system glucitol/sorbitol-specific EIIB component
    • Protein or peptide: PTS system glucitol/sorbitol-specific EIIC component
  • Ligand: sorbitol

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Supramolecule #1: Gut transporter with sorbitol

SupramoleculeName: Gut transporter with sorbitol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: strain K12

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Macromolecule #1: PTS system glucitol/sorbitol-specific EIIB component

MacromoleculeName: PTS system glucitol/sorbitol-specific EIIB component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: protein-Npi-phosphohistidine-D-sorbitol phosphotransferase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 33.359898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTHIRIEKGT GGWGGPLELK ATPGKKIVYI TAGTRPAIVD KLAQLTGWQA IDGFKEGEPA EAEIGVAVID CGGTLRCGIY PKRRIPTIN IHSTGKSGPL AQYIVEDIYV SGVKEENITV VGDATPQPSS VGRDYDTSKK ITEQSDGLLA KVGMGMGSTV A VLFQSGRD ...String:
MTHIRIEKGT GGWGGPLELK ATPGKKIVYI TAGTRPAIVD KLAQLTGWQA IDGFKEGEPA EAEIGVAVID CGGTLRCGIY PKRRIPTIN IHSTGKSGPL AQYIVEDIYV SGVKEENITV VGDATPQPSS VGRDYDTSKK ITEQSDGLLA KVGMGMGSTV A VLFQSGRD TIDTVLKTIL PFMAFVSALI GIIMASGLGD WIAHGLAPLA SHPLGLVMLA LICSFPLLSP FLGPGAVIAQ VI GVLIGVQ IGLGNIPPHL ALPALFAINA QAACDFIPVG LSLAEARQDT VRVGVPSVLV SRFLTGAPTV LIAWFVSGFI YQ

UniProtKB: PTS system glucitol/sorbitol-specific EIIB component

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Macromolecule #2: PTS system glucitol/sorbitol-specific EIIC component

MacromoleculeName: PTS system glucitol/sorbitol-specific EIIC component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 20.597262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIETITHGAE WFIGLFQKGG EVFTGMVTGI LPLLISLLVI MNALINFIGQ HRIERFAQRC AGNPVSRYLL LPCIGTFVFC NPMTLSLGR FMPEKYKPSY YAAASYSCHS MNGLFPHINP GELFVYLGIA SGLTTLNLPL GPLAVSYLLV GLVTNFFRGW V TDLTTAIF EKKMGIQLEQ KVHLAGATS

UniProtKB: PTS system glucitol/sorbitol-specific EIIC component

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Macromolecule #3: sorbitol

MacromoleculeName: sorbitol / type: ligand / ID: 3 / Number of copies: 3 / Formula: SOR
Molecular weightTheoretical: 182.172 Da
Chemical component information

ChemComp-SOR:
sorbitol

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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

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 237825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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