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- EMDB-18640: Cryo-EM structure of the glucose-specific PTS transporter IICB fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-18640
TitleCryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-open state
Map dataCryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-open state
Sample
  • Complex: Homo-dimeric complex
    • Protein or peptide: PTS system glucose-specific EIICB component
  • Ligand: beta-D-glucopyranose
Keywordsglucose transport protein / membrane protein / 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 import across plasma membrane / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / regulation of DNA-templated transcription ...protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / D-glucose import across plasma membrane / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
Phosphotransferase system, maltose/glucose-specific subfamily IIC component / 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. ...Phosphotransferase system, maltose/glucose-specific subfamily IIC component / 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 speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsRoth P / Fotiadis D / Jeckelmann J-M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation184980 Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Structure and mechanism of a phosphotransferase system glucose transporter.
Authors: Patrick Roth / Jean-Marc Jeckelmann / Inken Fender / Zöhre Ucurum / Thomas Lemmin / Dimitrios Fotiadis /
Abstract: Glucose is the primary source of energy for many organisms and is efficiently taken up by bacteria through a dedicated transport system that exhibits high specificity. In Escherichia coli, the ...Glucose is the primary source of energy for many organisms and is efficiently taken up by bacteria through a dedicated transport system that exhibits high specificity. In Escherichia coli, the glucose-specific transporter IICB serves as the major glucose transporter and functions as a component of the phosphoenolpyruvate-dependent phosphotransferase system. Here, we report cryo-electron microscopy (cryo-EM) structures of the glucose-bound IICB protein. The dimeric transporter embedded in lipid nanodiscs was captured in the occluded, inward- and occluded, outward-facing conformations. Together with biochemical and biophysical analyses, and molecular dynamics (MD) simulations, we provide insights into the molecular basis and dynamics for substrate recognition and binding, including the gates regulating the binding sites and their accessibility. By combination of these findings, we present a mechanism for glucose transport across the plasma membrane. Overall, this work provides molecular insights into the structure, dynamics, and mechanism of the IICB transporter in a native-like lipid environment.
History
DepositionOct 11, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18640.png

Downloads & links

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Map

FileDownload / File: emd_18640.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 240 pix.
= 232.2 Å		0.97 Å/pix.
x 240 pix.
= 232.2 Å		0.97 Å/pix.
x 240 pix.
= 232.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.075785436 - 1.6241275
Average (Standard dev.)0.0006980256 (±0.015782544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 232.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18640_msk_1.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 : Homo-dimeric complex

EntireName: Homo-dimeric complex
Components
  • Complex: Homo-dimeric complex
    • Protein or peptide: PTS system glucose-specific EIICB component
  • Ligand: beta-D-glucopyranose

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Supramolecule #1: Homo-dimeric complex

SupramoleculeName: Homo-dimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 53.44118 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFKNAFANLQ KVGKSLMLPV SVLPIAGILL GVGSANFSWL PAVVSHVMAE AGGSVFANMP LIFAIGVALG FTNNDGVSAL AAVVAYGIM VKTMAVVAPL VLHLPAEEIA SKHLADTGVL GGIISGAIAA YMFNRFYRIK LPEYLGFFAG KRFVPIISGL A AIFTGVVL ...String:
MFKNAFANLQ KVGKSLMLPV SVLPIAGILL GVGSANFSWL PAVVSHVMAE AGGSVFANMP LIFAIGVALG FTNNDGVSAL AAVVAYGIM VKTMAVVAPL VLHLPAEEIA SKHLADTGVL GGIISGAIAA YMFNRFYRIK LPEYLGFFAG KRFVPIISGL A AIFTGVVL SFIWPPIGSA IQTFSQWAAY QNPVVAFGIY GFIERCLVPF GLHHIWNVPF QMQIGEYTNA AGQVFHGDIP RY MAGDPTA GKLSGGFLFK MYGLPAAAIA IWHSAKPENR AKVGGIMISA ALTSFLTGIT EPIEFSFMFV APILYIIHAI LAG LAFPIC ILLGMRDGTS FSHGLIDFIV LSGNSSKLWL FPIVGIGYAI VYYTIFRVLI KALDLKTPGR EDATEDAKAT GTSE MAPAL VAAFGGKENI TNLDACITRL RVSVADVSKV DQAGLKKLGA AGVVVAGSGV QAIFGTKSDN LKTEMDEYIR NHLEL EVLF QGPVDHHHHH HHHHH

UniProtKB: PTS system glucose-specific EIICB component

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Macromolecule #2: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 2 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMHEPES-NaOH
100.0 mMNaCl
5.0 mMD-glucose
0.1 %Glycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 22 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12348 / Average exposure time: 1.232 sec. / Average electron dose: 60.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4474138
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 237565
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8qsr:
Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-facing conformation

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