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- PDB-4zwb: Crystal structure of maltose-bound human GLUT3 in the outward-occ... -

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Basic information

Entry
Database: PDB / ID: 4zwb
TitleCrystal structure of maltose-bound human GLUT3 in the outward-occluded conformation at 2.4 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 / 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. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / 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. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / 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
alpha-maltose / Solute carrier family 2, facilitated glucose transporter member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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)56,8172
Polymers56,4741
Non-polymers3421
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint1 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.460, 119.487, 53.908
Angle α, β, γ (deg.)90.00, 103.75, 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 38-40% PEG 400, 100 mM Mg (CHO2)2, 50 mM maltose, 100 mM ADA

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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 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 22422 / % possible obs: 94.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.6 / % possible all: 91.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZW9

4zw9


Resolution: 2.4→33.272 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1145 5.11 %
Rwork0.181 --
obs0.1832 22393 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→33.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 23 36 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083698
X-RAY DIFFRACTIONf_angle_d1.0865021
X-RAY DIFFRACTIONf_dihedral_angle_d14.0241316
X-RAY DIFFRACTIONf_chiral_restr0.039596
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3808-2.48910.23911200.17982424X-RAY DIFFRACTION86
2.4891-2.62030.21991390.17272683X-RAY DIFFRACTION95
2.6203-2.78440.24131620.17772693X-RAY DIFFRACTION96
2.7844-2.99920.21661370.16632743X-RAY DIFFRACTION96
2.9992-3.30080.24661470.18632693X-RAY DIFFRACTION96
3.3008-3.77790.2081520.18382703X-RAY DIFFRACTION96
3.7779-4.75750.21771390.18952666X-RAY DIFFRACTION94
4.7575-33.27520.22321490.17782643X-RAY DIFFRACTION92

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