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- PDB-4yb9: Crystal structure of the Bovine Fructose transporter GLUT5 in an ... -

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Basic information

Entry
Database: PDB / ID: 4yb9
TitleCrystal structure of the Bovine Fructose transporter GLUT5 in an open inward-facing conformation
ComponentsSolute carrier family 2, facilitated glucose transporter member 5
KeywordsTRANSPORT PROTEIN / GLUT5 Transporter / Fructose / Bovine MFS / Open Inward-facing conformation
Function / homology
Function and homology information


Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / cellular response to fructose stimulus / response to fructose / Neutrophil degranulation / sarcolemma ...Intestinal hexose absorption / regulation of systemic arterial blood pressure mediated by a chemical signal / fructose transmembrane transporter activity / fructose import across plasma membrane / fructose transmembrane transport / fructose binding / cellular response to fructose stimulus / response to fructose / Neutrophil degranulation / sarcolemma / apical plasma membrane / plasma membrane
Similarity search - Function
Fructose transporter, type 5 (GLUT5) / 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 / Growth Hormone; Chain: A; ...Fructose transporter, type 5 (GLUT5) / 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 / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Solute carrier family 2, facilitated glucose transporter member 5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVerdon, G. / Kang, H.J. / Iwata, S. / Drew, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/G02325/1 United Kingdom
Wellcome Trust062164/Z/00/Z United Kingdom
CitationJournal: Nature / Year: 2015
Title: Structure and mechanism of the mammalian fructose transporter GLUT5.
Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. ...Authors: Nomura, N. / Verdon, G. / Kang, H.J. / Shimamura, T. / Nomura, Y. / Sonoda, Y. / Hussien, S.A. / Qureshi, A.A. / Coincon, M. / Sato, Y. / Abe, H. / Nakada-Nakura, Y. / Hino, T. / Arakawa, T. / Kusano-Arai, O. / Iwanari, H. / Murata, T. / Kobayashi, T. / Hamakubo, T. / Kasahara, M. / Iwata, S. / Drew, D.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 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

Downloads & links

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Assembly

Deposited unit
D: Solute carrier family 2, facilitated glucose transporter member 5


Theoretical massNumber of molelcules
Total (without water)52,9461
Polymers52,9461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.610, 112.150, 139.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 5 / Fructose transporter / Glucose transporter type 5 / small intestine / GLUT-5


Mass: 52946.023 Da / Num. of mol.: 1 / Mutation: N51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SLC2A5, GLUT5 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P58353

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: PEG 300, Hepes, Lithium Sulfate, Sodium Chloride, HEGA-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→33.317 Å / Num. obs: 13346 / % possible obs: 66.99 % / Redundancy: 10.2 % / Rsym value: 0.101 / Net I/σ(I): 11.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.97

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rat GLUT5 crystal structure

Resolution: 3.2→33.317 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2581 1331 9.97 %
Rwork0.2368 --
obs0.2388 13346 66.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→33.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 0 3379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033460
X-RAY DIFFRACTIONf_angle_d0.94714
X-RAY DIFFRACTIONf_dihedral_angle_d13.0741208
X-RAY DIFFRACTIONf_chiral_restr0.037560
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2005-3.31480.3655280.3285223X-RAY DIFFRACTION13
3.3148-3.44740.3488440.2995335X-RAY DIFFRACTION19
3.4474-3.60410.3242600.2723487X-RAY DIFFRACTION28
3.6041-3.79390.2511870.2477721X-RAY DIFFRACTION41
3.7939-4.03120.29211240.24261175X-RAY DIFFRACTION66
4.0312-4.34180.24081960.21651793X-RAY DIFFRACTION100
4.3418-4.77760.24942030.18321764X-RAY DIFFRACTION100
4.7776-5.46630.21251960.18921808X-RAY DIFFRACTION100
5.4663-6.8770.28511890.25671845X-RAY DIFFRACTION100
6.877-33.3190.26262040.26741864X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 26.9302 Å / Origin y: -11.3213 Å / Origin z: -36.1469 Å
111213212223313233
T0.8499 Å20.0769 Å2-0.0054 Å2-0.7974 Å20.0794 Å2--0.9795 Å2
L4.4359 °2-0.6924 °22.5774 °2-13.4355 °20.7271 °2--8.6792 °2
S0.077 Å °-0.1985 Å °0.0655 Å °-0.269 Å °-0.4498 Å °1.7636 Å °-0.0068 Å °-0.8322 Å °0.0701 Å °
Refinement TLS groupSelection details: all

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