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- PDB-4zw9: Crystal structure of human GLUT3 bound to D-glucose in the outwar... -

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Basic information

Entry
Database: PDB / ID: 4zw9
TitleCrystal structure of human GLUT3 bound to D-glucose in the outward-occluded conformation at 1.5 angstrom
ComponentsSolute carrier family 2, facilitated glucose transporter member 3
KeywordsTRANSPORT PROTEIN / 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 / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain ...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 / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / 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: 1.502 Å
AuthorsDeng, D. / Sun, P.C. / Yan, C.Y. / Yan, N.
CitationJournal: Nature / Year: 2015
Title: Molecular basis of ligand recognition and transport by glucose transporters
Authors: Deng, D. / Sun, P.C. / Yan, C.Y. / Ke, M. / Jiang, X. / Xiong, L. / Ren, W. / Hirata, K. / Yamamoto, M. / Fan, S. / Yan, N.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)57,9046
Polymers56,4741
Non-polymers1,4305
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint8 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.338, 118.132, 51.341
Angle α, β, γ (deg.)90.00, 102.67, 90.00
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-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: isolated from a genetically manipulated source
Formula: C6H12O6
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.8
Details: 28%(v/v) PEG400, 0.1M HEPES, 50 mM ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 88120 / % possible obs: 98.8 % / Redundancy: 18 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.6 / % possible all: 91.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pyp

4pyp


Resolution: 1.502→30.226 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 4233 4.81 %
Rwork0.1836 --
obs0.1843 88058 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.502→30.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 99 101 3807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093820
X-RAY DIFFRACTIONf_angle_d1.1325170
X-RAY DIFFRACTIONf_dihedral_angle_d15.2511394
X-RAY DIFFRACTIONf_chiral_restr0.046608
X-RAY DIFFRACTIONf_plane_restr0.007643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5016-1.51860.2651170.26512471X-RAY DIFFRACTION86
1.5186-1.53650.24421370.24982552X-RAY DIFFRACTION92
1.5365-1.55520.25591260.2452692X-RAY DIFFRACTION93
1.5552-1.57490.26731380.23182653X-RAY DIFFRACTION96
1.5749-1.59570.211490.23712739X-RAY DIFFRACTION97
1.5957-1.61750.22371570.22422745X-RAY DIFFRACTION98
1.6175-1.64060.2311380.21882813X-RAY DIFFRACTION99
1.6406-1.66510.22331300.20392814X-RAY DIFFRACTION99
1.6651-1.69110.21451330.2032816X-RAY DIFFRACTION100
1.6911-1.71880.2251450.19952819X-RAY DIFFRACTION100
1.7188-1.74850.1861190.19152844X-RAY DIFFRACTION100
1.7485-1.78030.20831460.18952864X-RAY DIFFRACTION100
1.7803-1.81450.20651420.18572798X-RAY DIFFRACTION100
1.8145-1.85150.2111510.17562815X-RAY DIFFRACTION100
1.8515-1.89180.18961330.17062855X-RAY DIFFRACTION100
1.8918-1.93580.15661240.16832857X-RAY DIFFRACTION100
1.9358-1.98420.20191620.16982793X-RAY DIFFRACTION100
1.9842-2.03780.19031420.16672831X-RAY DIFFRACTION100
2.0378-2.09780.18091290.16512846X-RAY DIFFRACTION100
2.0978-2.16550.16431420.1572833X-RAY DIFFRACTION100
2.1655-2.24280.17261710.15642815X-RAY DIFFRACTION100
2.2428-2.33260.15731530.15752810X-RAY DIFFRACTION100
2.3326-2.43870.17621280.16052863X-RAY DIFFRACTION100
2.4387-2.56720.17051210.16062875X-RAY DIFFRACTION100
2.5672-2.7280.16381460.16662809X-RAY DIFFRACTION100
2.728-2.93850.16591360.16352826X-RAY DIFFRACTION100
2.9385-3.23390.18771500.17382870X-RAY DIFFRACTION100
3.2339-3.70110.20451800.18252805X-RAY DIFFRACTION100
3.7011-4.66020.2181500.19072835X-RAY DIFFRACTION100
4.6602-30.23230.24071380.21692867X-RAY DIFFRACTION99

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