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- PDB-4zwc: Crystal structure of maltose-bound human GLUT3 in the outward-ope... -

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Basic information

Entry
Database: PDB / ID: 4zwc
TitleCrystal structure of maltose-bound human GLUT3 in the outward-open conformation at 2.6 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
alpha-maltose / (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: 2.6 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
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

Downloads & links

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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)114,7037
Polymers112,9492
Non-polymers1,7545
Water93752
1
A: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5304
Polymers56,4741
Non-polymers1,0553
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)57,1733
Polymers56,4741
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.109, 121.880, 96.078
Angle α, β, γ (deg.)90.00, 108.14, 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.: 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.9
Details: 34% PEG 400, 400 mM (NH4)2HPO4, 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 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 49602 / % possible obs: 95 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.6 / % possible all: 97.3

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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: 2.6→31.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2477 5 %
Rwork0.215 --
obs0.217 49536 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7186 0 121 52 7359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017516
X-RAY DIFFRACTIONf_angle_d1.2610167
X-RAY DIFFRACTIONf_dihedral_angle_d16.3362727
X-RAY DIFFRACTIONf_chiral_restr0.0521197
X-RAY DIFFRACTIONf_plane_restr0.0071262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.603-2.65310.28521200.2492488X-RAY DIFFRACTION90
2.6531-2.70720.29041410.2442696X-RAY DIFFRACTION97
2.7072-2.7660.24981420.23682686X-RAY DIFFRACTION98
2.766-2.83030.2631120.23012737X-RAY DIFFRACTION98
2.8303-2.90110.2481550.23172681X-RAY DIFFRACTION98
2.9011-2.97940.24811440.22562665X-RAY DIFFRACTION97
2.9794-3.06710.30621490.23272678X-RAY DIFFRACTION97
3.0671-3.1660.29061520.2372660X-RAY DIFFRACTION97
3.166-3.2790.26161300.22962727X-RAY DIFFRACTION98
3.279-3.41010.27461540.22222660X-RAY DIFFRACTION97
3.4101-3.56510.25711490.21572686X-RAY DIFFRACTION97
3.5651-3.75280.24751370.22292665X-RAY DIFFRACTION97
3.7528-3.98750.24721640.21482671X-RAY DIFFRACTION97
3.9875-4.29470.25441470.21582671X-RAY DIFFRACTION97
4.2947-4.72570.3106760.24241598X-RAY DIFFRACTION57
4.7257-5.40650.2311290.21332681X-RAY DIFFRACTION96
5.4065-6.80060.24261390.21232723X-RAY DIFFRACTION97
6.8006-31.69980.18041370.15232686X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -60.0423 Å / Origin y: 35.6376 Å / Origin z: -9.4388 Å
111213212223313233
T0.376 Å2-0.0113 Å20.0127 Å2-0.3757 Å2-0.0153 Å2--0.3728 Å2
L0.1845 °2-0.203 °20.1715 °2-0.3947 °2-0.3296 °2--0.3374 °2
S0.0108 Å °0.0266 Å °-0.0055 Å °-0.0311 Å °-0 Å °0.0398 Å °0.0147 Å °0.0143 Å °-0.0223 Å °
Refinement TLS groupSelection details: ALL

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