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- PDB-9x2m: Gut transporter with sorbitol -

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Basic information

Entry
Database: PDB / ID: 9x2m
TitleGut transporter with sorbitol
Components
  • PTS system glucitol/sorbitol-specific EIIB component
  • PTS system glucitol/sorbitol-specific EIIC component
KeywordsTRANSPORT PROTEIN / sugar phosphotransferase system / PTS / glucitol/sorbitol / PTS Gut family
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
sorbitol / PTS system glucitol/sorbitol-specific EIIC component / PTS system glucitol/sorbitol-specific EIIB component
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsDeng, T. / Ge, X. / Wang, J.
Funding support China, 3items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data 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
1: PTS system glucitol/sorbitol-specific EIIB component
2: PTS system glucitol/sorbitol-specific EIIC component
A: PTS system glucitol/sorbitol-specific EIIC component
B: PTS system glucitol/sorbitol-specific EIIC component
E: PTS system glucitol/sorbitol-specific EIIB component
F: PTS system glucitol/sorbitol-specific EIIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4189
Polymers161,8716
Non-polymers5473
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 PTS system glucitol/sorbitol-specific EIIB component / EII-Gut / Enzyme II-Gut / Glucitol/sorbitol-specific phosphotransferase enzyme IIB component


Mass: 33359.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: srlE, gutA, gutE, b2703, JW5430 / Production host: Escherichia coli (E. coli)
References: UniProt: P56580, protein-Npi-phosphohistidine-D-sorbitol phosphotransferase
#2: Protein PTS system glucitol/sorbitol-specific EIIC component / EIIC-Gut / Glucitol/sorbitol permease IIC component


Mass: 20597.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: srlA, gutA, sbl, b2702, JW5429 / Production host: Escherichia coli (E. coli) / References: UniProt: P56579
#3: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Gut transporter with sorbitol / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli) / Strain: strain K12
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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 Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 48.23 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237825 / Symmetry type: POINT
RefinementHighest resolution: 3.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088075
ELECTRON MICROSCOPYf_angle_d0.94411005
ELECTRON MICROSCOPYf_dihedral_angle_d4.6021104
ELECTRON MICROSCOPYf_chiral_restr0.0411322
ELECTRON MICROSCOPYf_plane_restr0.0081365

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