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- EMDB-54787: Cryo-EM structure of PfHT1 bound to 2,5-anhydro-D-mannitol -

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Basic information

Entry
Database: EMDB / ID: EMD-54787
TitleCryo-EM structure of PfHT1 bound to 2,5-anhydro-D-mannitol
Map data
Sample
  • Complex: PfHT1 dimer with 2,5-anhydro-D-mannitol
    • Protein or peptide: Hexose transporter 1,Green fluorescent protein
  • Ligand: 2.5-anhydro-D-mannitol
KeywordsSugar transporter / Plasmodium falciparum hexose transporter 1 / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsGulati A / Suades A / Drew D
Funding support Sweden, Denmark, 3 items
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, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54787.png

Downloads & links

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Map

FileDownload / File: emd_54787.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 412 pix.
= 267.8 Å		0.65 Å/pix.
x 412 pix.
= 267.8 Å		0.65 Å/pix.
x 412 pix.
= 267.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.17226924 - 0.42972988
Average (Standard dev.)0.0000981436 (±0.008894771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 267.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54787_msk_1.map
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Half map: #1

Fileemd_54787_half_map_1.map
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Half map: #2

Fileemd_54787_half_map_2.map
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Sample components

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Entire : PfHT1 dimer with 2,5-anhydro-D-mannitol

EntireName: PfHT1 dimer with 2,5-anhydro-D-mannitol
Components
  • Complex: PfHT1 dimer with 2,5-anhydro-D-mannitol
    • Protein or peptide: Hexose transporter 1,Green fluorescent protein
  • Ligand: 2.5-anhydro-D-mannitol

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Supramolecule #1: PfHT1 dimer with 2,5-anhydro-D-mannitol

SupramoleculeName: PfHT1 dimer with 2,5-anhydro-D-mannitol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: Hexose transporter 1,Green fluorescent protein

MacromoleculeName: Hexose transporter 1,Green fluorescent protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 84.639891 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEKEDSGFFS TSFKYVLSAC IASFIFGYQV SVLNTIKNFI VVEFEWCKGE KDRLNCSNNT IQSSFLLASV FIGAVLGCGF SGYLVQFGR RLSLLIIYNF FFLVSILTSI THHFHTILFA RLLSGFGIGL VTVSVPMYIS EMTHKDKKGA YGVMHQLFIT F GIFVAVML ...String:
MEKEDSGFFS TSFKYVLSAC IASFIFGYQV SVLNTIKNFI VVEFEWCKGE KDRLNCSNNT IQSSFLLASV FIGAVLGCGF SGYLVQFGR RLSLLIIYNF FFLVSILTSI THHFHTILFA RLLSGFGIGL VTVSVPMYIS EMTHKDKKGA YGVMHQLFIT F GIFVAVML GLAMGEGPKA DSTEPLTSFA KLWWRLMFLF PSVISLIGIL ALVVFFKEET PYFLFEKGRI EESKNILKKI YE TDNVDEP LNAIKEAVEQ NESAKKNSLS LLSALKIPSY RYVIILGCLL SGLQQFTGIN VLVSNSNELY KEFLDSHLIT ILS VVMTAV NFLMTFPAIY IVEKLGRKTL LLWGCVGVLV AYLPTAIANE INRNSNFVKI LSIVATFVMI ISFAVSYGPV LWIY LHEMF PSEIKDSAAS LASLVNWVCA IIVVFPSDII IKKSPSILFI VFSVMSILTF FFIFFFIKET KGGEIGTSPY ITMEE RQKH MTKSVVENLY FQGQFSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVT TFG YGVQCFARYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLVNRIEL KGIDFKEDGN ILGHKLE YN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHYLSTQ SALSKDPNEK RDHMVLLE F VTAAGITHGM DELYKDELYK HHHHHHHH

UniProtKB: Hexose transporter 1, Green fluorescent protein

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Macromolecule #2: 2.5-anhydro-D-mannitol

MacromoleculeName: 2.5-anhydro-D-mannitol / type: ligand / ID: 2 / Number of copies: 2 / Formula: A1IVP
Molecular weightTheoretical: 164.156 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 300678
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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