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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: To Be Published
Title: A Two-step Mechanism for Sugar Transport
Authors: Ahn, D. / Reichenbach, T. / Alleva, C. / Ruda, A. / Gulati, A. / Bonaccorsi, M. / Claesson, M. / Suades, A. / Delemotte, L. / Widmalm, G. / Drew, D.
History
DepositionAug 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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
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
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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