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- PDB-7crz: Crystal structure of human glucose transporter GLUT3 bound with C3361 -

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Basic information

Entry
Database: PDB / ID: 7crz
TitleCrystal structure of human glucose transporter GLUT3 bound with C3361
ComponentsSolute carrier family 2, facilitated glucose transporter member 3
KeywordsTRANSPORT PROTEIN / MFS / hexose transporter / inhibitor / Plasmodium falciparum
Function / homology
Function and homology information


galactose transmembrane transporter activity / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / galactose transmembrane transport / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Cellular hexose transport / Vitamin C (ascorbate) metabolism / glucose import across plasma membrane / L-ascorbic acid metabolic process ...galactose transmembrane transporter activity / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / galactose transmembrane transport / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Cellular hexose transport / Vitamin C (ascorbate) metabolism / glucose import across plasma membrane / L-ascorbic acid metabolic process / glucose transmembrane transport / D-glucose binding / aggresome / glucose import / tertiary granule membrane / ficolin-1-rich granule membrane / transport across blood-brain barrier / specific granule membrane / MECP2 regulates neuronal receptors and channels / secretory granule membrane / cell projection / perikaryon / carbohydrate metabolic process / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Glucose transporter, type 3 (GLUT3) / Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Chem-F00 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Solute carrier family 2, facilitated glucose transporter member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuan, Y.Y. / Zhang, S. / Wang, N. / Jiang, X. / Yan, N.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31630017 China
National Science Foundation (NSF, China)81861138009 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Orthosteric-allosteric dual inhibitors of PfHT1 as selective antimalarial agents.
Authors: Huang, J. / Yuan, Y. / Zhao, N. / Pu, D. / Tang, Q. / Zhang, S. / Luo, S. / Yang, X. / Wang, N. / Xiao, Y. / Zhang, T. / Liu, Z. / Sakata-Kato, T. / Jiang, X. / Kato, N. / Yan, N. / Yin, H.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9468
Polymers56,4741
Non-polymers2,4727
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18730 Å2
Unit cell
Length a, b, c (Å)48.329, 118.248, 54.252
Angle α, β, γ (deg.)90.000, 103.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 3 / / Glucose transporter type 3 / brain / GLUT-3


Mass: 56474.492 Da / Num. of mol.: 1 / Mutation: N43T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A3, GLUT3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11169
#2: Chemical ChemComp-F00 / (2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4-undec-10-enoxy-oxane-2,3,5-triol


Mass: 332.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 0.1 M NH4Cl, 0.1 M HEPES pH 7.0, 40% PEG 400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26341 / % possible obs: 99.9 % / Redundancy: 99.2 % / CC1/2: 0.999 / Net I/σ(I): 8.57
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 3132 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZW9

4zw9


Resolution: 2.3→19.806 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1320 5.03 %
Rwork0.1657 24943 -
obs0.168 26263 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.68 Å2 / Biso mean: 35.98 Å2 / Biso min: 18.71 Å2
Refinement stepCycle: final / Resolution: 2.3→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 173 135 3907
Biso mean--54.15 45.31 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063858
X-RAY DIFFRACTIONf_angle_d0.975190
X-RAY DIFFRACTIONf_chiral_restr0.037600
X-RAY DIFFRACTIONf_plane_restr0.005630
X-RAY DIFFRACTIONf_dihedral_angle_d15.2671438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.3920.2431370.20122753
2.392-2.50060.271500.1842756
2.5006-2.63220.24341420.1692775
2.6322-2.79670.20631520.1552753
2.7967-3.01190.17771430.14692791
3.0119-3.31370.21011460.15742741
3.3137-3.79030.19211450.16112790
3.7903-4.76440.20991450.1632783
4.7644-19.8060.21331600.17262801

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