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- PDB-9u82: Cryo-EM structure of Leminorella grimontii GatC in the presence o... -

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Basic information

Entry
Database: PDB / ID: 9u82
TitleCryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose
ComponentsPTS galactitol transporter subunit IIC
KeywordsTRANSPORT PROTEIN / PTS / D-xylose / transporter
Function / homologygalactitol transmembrane transporter activity / Galactitol permease IIC component / Phosphotransferase system, sugar-specific permease component / PTS system sugar-specific permease component / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / phosphoenolpyruvate-dependent sugar phosphotransferase system / plasma membrane / PTS galactitol transporter subunit IIC
Function and homology information
Biological speciesLeminorella grimontii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsTakahashi, Y.S. / Kohga, H. / Shigematsu, H. / Miyazaki, R. / Tsukazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis of a phosphotransferase system xylose transporter
Authors: Takahashi, Y.S. / Kohga, H. / Chek, M.F. / Yamamoto, K. / Takahashi, J.F. / Shigematsu, H. / Tanaka, Y. / Ichikawa, M. / Miyazaki, R. / Hakoshima, T. / Tsukazaki, T.
History
DepositionMar 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 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
A: PTS galactitol transporter subunit IIC
B: PTS galactitol transporter subunit IIC


Theoretical massNumber of molelcules
Total (without water)100,1562
Polymers100,1562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein PTS galactitol transporter subunit IIC


Mass: 50078.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leminorella grimontii (bacteria) / Gene: SOASR030_34840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAV5N9B3
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: GatC bound to D-xylose / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Leminorella grimontii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7 / Details: 300mM NaCl, 50mM HEPES-NaOH (pH7.0), 10mM D-xylose
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.92 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
7PHENIX1.21.1_5286model fitting
9PHENIX1.21.1_5286model refinement
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2480272
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 442864 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056850
ELECTRON MICROSCOPYf_angle_d0.589332
ELECTRON MICROSCOPYf_dihedral_angle_d3.517934
ELECTRON MICROSCOPYf_chiral_restr0.0431152
ELECTRON MICROSCOPYf_plane_restr0.0041146

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