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- PDB-5c65: Structure of the human glucose transporter GLUT3 / SLC2A3 -

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Basic information

Entry
Database: PDB / ID: 5c65
TitleStructure of the human glucose transporter GLUT3 / SLC2A3
ComponentsSolute carrier family 2, facilitated glucose transporter member 3
KeywordsTRANSPORT PROTEIN / MEMBRANE TRANSPORTER / SUGAR TRANSPORT / Structural Genomics / Structural Genomics Consortium / SGC
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
Octyl Glucose Neopentyl Glycol / CHOLESTEROL HEMISUCCINATE / Solute carrier family 2, facilitated glucose transporter member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPike, A.C.W. / Quigley, A. / Chu, A. / Tessitore, A. / Xia, X. / Mukhopadhyay, S. / Wang, D. / Kupinska, K. / Strain-Damerell, C. / Chalk, R. ...Pike, A.C.W. / Quigley, A. / Chu, A. / Tessitore, A. / Xia, X. / Mukhopadhyay, S. / Wang, D. / Kupinska, K. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of the human glucose transporter GLUT3 / SLC2A3
Authors: Pike, A.C.W. / Quigley, A. / Chu, A. / Tessitore, A. / Xia, X. / Mukhopadhyay, S. / Wang, D. / Kupinska, K. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / ...Authors: Pike, A.C.W. / Quigley, A. / Chu, A. / Tessitore, A. / Xia, X. / Mukhopadhyay, S. / Wang, D. / Kupinska, K. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,13013
Polymers105,0392
Non-polymers6,09211
Water48627
1
A: Solute carrier family 2, facilitated glucose transporter member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4188
Polymers52,5191
Non-polymers3,8997
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)54,7125
Polymers52,5191
Non-polymers2,1934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.550, 116.030, 99.750
Angle α, β, γ (deg.)90.00, 106.91, 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: 52519.262 Da / Num. of mol.: 2 / Fragment: UNP residues 1-474 / Mutation: N43Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A3, GLUT3 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11169
#2: Chemical
ChemComp-37X / Octyl Glucose Neopentyl Glycol


Mass: 568.695 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C27H52O12
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M citrate pH 5.5, 29% PEG400, 0.1M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.65→73.71 Å / Num. obs: 40188 / % possible obs: 99.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 82.25 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.8
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 1.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
xia20.3.6.3data reduction
Aimless0.5.9data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PYP

4pyp


Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.9045 / Cor.coef. Fo:Fc free: 0.9089 / SU R Cruickshank DPI: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2006 5 %RANDOM
Rwork0.2054 ---
obs0.2062 40153 99.76 %-
Displacement parametersBiso mean: 102.93 Å2
Baniso -1Baniso -2Baniso -3
1--8.1544 Å20 Å2-20.9043 Å2
2--1.7267 Å20 Å2
3---6.4277 Å2
Refine analyzeLuzzati coordinate error obs: 0.485 Å
Refinement stepCycle: 1 / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6786 0 418 27 7231
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097365HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0210025HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3400SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1040HARMONIC5
X-RAY DIFFRACTIONt_it7365HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1066SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9072SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2472 155 5.3 %
Rwork0.2275 2770 -
all0.2285 2925 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.9030.3364-0.67482.0720.01573.28610.00330.1711-0.0451-0.5326-0.0491-0.0128-0.1028-0.28280.0458-0.0091-0.00580.081-0.3602-0.0037-0.1614Chain A-0.9508-7.3603-55.7809
23.95250.096-0.42231.41110.13074.79790.1801-1.19130.20650.0931-0.1168-0.0643-0.447-0.0117-0.0633-0.3635-0.10150.04980.1017-0.0933-0.3386Chain B-12.3027-6.1748-12.0055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1all{A|5 - 469}A5 - 469
2X-RAY DIFFRACTION2all{B|6 - 469}B6 - 469

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