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- PDB-7sps: Crystal structure of human glucose transporter GLUT3 bound with e... -

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Basic information

Entry
Database: PDB / ID: 7sps
TitleCrystal structure of human glucose transporter GLUT3 bound with exofacial inhibitor SA47
ComponentsSolute carrier family 2, facilitated glucose transporter member 3
KeywordsTRANSPORT PROTEIN/INHIBITOR / MFS / hexose transporter / inhibitor / TRANSPORT PROTEIN-INHIBITOR complex
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 / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Cellular hexose transport / glucose import across plasma membrane ...galactose transmembrane transporter activity / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / galactose transmembrane transport / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Cellular hexose transport / glucose import across plasma membrane / glucose transmembrane transport / glucose binding / aggresome / glucose import / tertiary granule membrane / transport across blood-brain barrier / ficolin-1-rich granule membrane / 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-A0E / (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
AuthorsWang, N. / Jiang, X. / Yan, N.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31630017 China
National Science Foundation (NSF, China)81861138009 China
National Science Foundation (NSF, China)31611130036 China
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for inhibiting human glucose transporters by exofacial inhibitors.
Authors: Wang, N. / Zhang, S. / Yuan, Y. / Xu, H. / Defossa, E. / Matter, H. / Besenius, M. / Derdau, V. / Dreyer, M. / Halland, N. / He, K.H. / Petry, S. / Podeschwa, M. / Tennagels, N. / Jiang, X. / Yan, N.
History
DepositionNov 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6389
Polymers113,8162
Non-polymers2,8227
Water2,126118
1
A: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1414
Polymers56,9081
Non-polymers1,2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4975
Polymers56,9081
Non-polymers1,5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.591, 121.552, 95.872
Angle α, β, γ (deg.)90.000, 108.140, 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: 56907.918 Da / Num. of mol.: 2 / 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-A0E / methyl N-[(2-{4-[4-(5-fluoro-2-methoxyphenyl)piperazin-1-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}phenyl)methyl]-beta-alaninate


Mass: 519.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30FN7O3 / 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.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.77 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 40% v/v PEG400, 100 mM sodium citrate, pH 5.7, 400 mM potassium formate

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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 30, 2019
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: 75008 / % possible obs: 99.9 % / Redundancy: 23.07 % / CC1/2: 0.998 / Net I/σ(I): 11.75
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 8977 / CC1/2: 0.536

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZW9
Resolution: 2.3→46.39 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.8 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 7424 5.03 %
Rwork0.2119 140136 -
obs0.213 74928 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.41 Å2 / Biso mean: 54.6828 Å2 / Biso min: 26.9 Å2
Refinement stepCycle: final / Resolution: 2.3→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 277 118 7563
Biso mean--64.62 50.63 -
Num. residues----936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.31162680.344664493299
2.33-2.350.3642540.33384649490399
2.35-2.380.33952360.33044632486899
2.38-2.410.34562380.323846914929100
2.41-2.440.3312530.300146674920100
2.44-2.480.36432260.287146374863100
2.48-2.510.29752270.280947504977100
2.51-2.550.28992490.276446184867100
2.55-2.590.28872620.263147645026100
2.59-2.630.2672470.264645954842100
2.63-2.680.32642390.24546954934100
2.68-2.730.24232250.232846964921100
2.73-2.780.25412410.22747695010100
2.78-2.840.27812320.214245944826100
2.84-2.90.20052450.20747595004100
2.9-2.970.24212830.199745864869100
2.97-3.040.23042380.209647284966100
3.04-3.120.24572900.21446494939100
3.12-3.210.27682590.220446744933100
3.21-3.320.2382700.212146564926100
3.32-3.440.21672350.195146864921100
3.44-3.570.23182180.191746994917100
3.57-3.740.20212440.185846494893100
3.74-3.930.22322270.200947104937100
3.93-4.180.21122870.198246824969100
4.18-4.50.23312210.203146844905100
4.5-4.950.24692100.2014675488599
4.95-5.670.19142840.198146254909100
5.67-7.140.20182630.194246814944100
7.14-46.390.17592530.15944572482598

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