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- PDB-9sdl: Cryo-EM structure of PfHT1 bound to 2,5-anhydro-D-mannitol -

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Basic information

Entry
Database: PDB / ID: 9sdl
TitleCryo-EM structure of PfHT1 bound to 2,5-anhydro-D-mannitol
ComponentsHexose transporter 1,Green fluorescent protein
KeywordsTRANSPORT PROTEIN / Sugar transporter / Plasmodium falciparum hexose transporter 1
Function / homology
Function and homology information


hexose transmembrane transporter activity / bioluminescence / generation of precursor metabolites and energy / plasma membrane
Similarity search - Function
Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily ...Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
: / Hexose transporter 1 / Green fluorescent protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsGulati, A. / Suades, A. / Drew, D.
Funding support Sweden, Denmark, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Novo Nordisk Foundation Denmark
Cancerfonden Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: A two-step mechanism for sugar translocation.
Authors: Do-Hwan Ahn / Claudia Alleva / Tom Reichenbach / Ashutosh Gulati / Alessandro Ruda / Marta Bonaccorsi / Jakob M Silberberg / Magnus Claesson / Albert Suades / Lucie Delemotte / Göran Widmalm / David Drew /
Abstract: In mammals, glucose transporters (GLUTs) mediate organism-wide sugar distribution, yet the molecular basis of substrate specificity remains unclear. The bacterial xylose transporter XylE serves as a ...In mammals, glucose transporters (GLUTs) mediate organism-wide sugar distribution, yet the molecular basis of substrate specificity remains unclear. The bacterial xylose transporter XylE serves as a model for GLUTs. However, although xylose and glucose bind with a similar affinity, xylose is transported, but glucose acts as an inhibitor. Here, using saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, we distinguished transported sugars from sugar inhibitors. Our findings revealed that only transported sugars generate STD NMR signals, which are abolished for xylose when XylE is trapped in either outward- or inward-facing conformations. Engineering the sugar-binding pocket and gating helix TM7b enabled glucose transport by XylE and corresponding STD signals. Using complementary molecular dynamics simulations, together with structural, biochemical and STD NMR analysis of related parasitic and mammalian GLUTs, we identified TM7b as a key determinant of occluded state formation. We conclude that, rather than the initial substrate-binding event observed in experimental structures, formation of a substrate-induced transition-state intermediate is the primary determinant of specificity in transporters.
History
DepositionAug 14, 2025Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexose transporter 1,Green fluorescent protein
B: Hexose transporter 1,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6084
Polymers169,2802
Non-polymers3282
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 22 - 492 / Label seq-ID: 8 - 478

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA

NCS oper: (Code: givenMatrix: (-0.999996234304, 0.00142393251924, -0.00234601660556), (-0.00142354715583, -0.999998972991, -0.000165924512733), (-0.00234625046149, -0.000162584222645, 0.999997234334) ...NCS oper: (Code: given
Matrix: (-0.999996234304, 0.00142393251924, -0.00234601660556), (-0.00142354715583, -0.999998972991, -0.000165924512733), (-0.00234625046149, -0.000162584222645, 0.999997234334)
Vector: 267.9762522, 268.005423227, 0.312800928047)

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Components

#1: Protein Hexose transporter 1,Green fluorescent protein


Mass: 84639.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum), (gene. exp.) Aequorea victoria (jellyfish)
Gene: ht1, GFP / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O97467, UniProt: P42212
#2: Sugar ChemComp-A1IVP / 2.5-anhydro-D-mannitol / (2~{R},3~{S},4~{S},5~{R})-2,5-bis(hydroxymethyl)oxolane-3,4-diol


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: PfHT1 dimer with 2,5-anhydro-D-mannitol / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 62.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300678 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00297790
ELECTRON MICROSCOPYf_angle_d0.424110556
ELECTRON MICROSCOPYf_chiral_restr0.03491250
ELECTRON MICROSCOPYf_plane_restr0.0031274
ELECTRON MICROSCOPYf_dihedral_angle_d3.4781006
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.00945823244E-12 Å

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