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- PDB-7spt: Crystal structure of exofacial state human glucose transporter GLUT3 -

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Basic information

Entry
Database: PDB / ID: 7spt
TitleCrystal structure of exofacial state human glucose transporter GLUT3
ComponentsSolute carrier family 2, facilitated glucose transporter member 3
KeywordsTRANSPORT PROTEIN / MFS / hexose transporter
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
alpha-D-glucopyranose / (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: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3305
Polymers57,0801
Non-polymers1,2504
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint3 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.231, 118.430, 53.728
Angle α, β, γ (deg.)90.000, 103.160, 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: 57080.105 Da / Num. of mol.: 1 / Mutation: N43T, S64W, I305W
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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 40% v/v PEG400, 100 mM Tris, pH 7.6, 100 mM magnesium chloride

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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 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34213 / % possible obs: 99.9 % / Redundancy: 13.49 % / CC1/2: 0.98 / Net I/σ(I): 6.34
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 4424 / CC1/2: 0.758

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Processing

Software
NameVersionClassification
PHENIXdev_2405refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZW9

4zw9


Resolution: 2.1→46.965 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1709 5 %
Rwork0.1767 32492 -
obs0.1788 34201 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.94 Å2 / Biso mean: 30.8672 Å2 / Biso min: 8.78 Å2
Refinement stepCycle: final / Resolution: 2.1→46.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 223 3844
Biso mean---45.14 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073790
X-RAY DIFFRACTIONf_angle_d0.7865123
X-RAY DIFFRACTIONf_chiral_restr0.047595
X-RAY DIFFRACTIONf_plane_restr0.006636
X-RAY DIFFRACTIONf_dihedral_angle_d14.2442210
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.16180.3221410.26512686
2.1618-2.23160.25411420.23392686
2.2316-2.31140.27451410.20122705
2.3114-2.40390.2391430.18242704
2.4039-2.51330.23021410.16372686
2.5133-2.64580.19221430.1612711
2.6458-2.81160.22871420.15772706
2.8116-3.02860.21131430.15262729
3.0286-3.33330.20641430.16332699
3.3333-3.81550.20031420.16152706
3.8155-4.80630.20851440.17672728
4.8063-46.9650.21161440.18412746
Refinement TLS params.Method: refined / Origin x: 91.1376 Å / Origin y: 8.7049 Å / Origin z: 114.1438 Å
111213212223313233
T0.1113 Å20.0037 Å2-0.0039 Å2-0.1079 Å20.0097 Å2--0.1025 Å2
L0.7349 °20.2268 °2-0.0237 °2-0.3822 °20.0784 °2--0.1793 °2
S-0.0097 Å °0.0096 Å °0.0411 Å °-0.0039 Å °-0.0285 Å °0.0091 Å °0.0099 Å °0.0041 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 504
2X-RAY DIFFRACTION1allS1 - 223

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