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- PDB-4pyp: Crystal structure of the human glucose transporter GLUT1 -

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Basic information

Entry
Database: PDB / ID: 4pyp
TitleCrystal structure of the human glucose transporter GLUT1
ComponentsSolute carrier family 2, facilitated glucose transporter member 1
KeywordsTRANSPORT PROTEIN / membrane transporter / helix / Glycosylation
Function / homology
Function and homology information


glucose transporter complex / Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) / long-chain fatty acid import across plasma membrane / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / Lactose synthesis / D-glucose transmembrane transporter activity / Cellular hexose transport / glucose transmembrane transporter activity ...glucose transporter complex / Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) / long-chain fatty acid import across plasma membrane / response to Thyroglobulin triiodothyronine / dehydroascorbic acid transmembrane transporter activity / dehydroascorbic acid transport / Lactose synthesis / D-glucose transmembrane transporter activity / Cellular hexose transport / glucose transmembrane transporter activity / glucose import across plasma membrane / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / glucose transmembrane transport / photoreceptor cell maintenance / cellular hyperosmotic response / female germ cell nucleus / female pronucleus / long-chain fatty acid transmembrane transporter activity / cortical actin cytoskeleton / glucose import / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / intercalated disc / cellular response to glucose starvation / photoreceptor inner segment / caveola / central nervous system development / Regulation of insulin secretion / female pregnancy / response to insulin / cerebral cortex development / sarcolemma / kinase binding / Z disc / cellular response to mechanical stimulus / : / melanosome / presynapse / midbody / protein-containing complex assembly / basolateral plasma membrane / blood microparticle / response to hypoxia / apical plasma membrane / Golgi membrane / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Glucose transporter, type 1 (GLUT1) / 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 1 (GLUT1) / 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
Solute carrier family 2, facilitated glucose transporter member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.166 Å
AuthorsDeng, D. / Yan, C.Y. / Xu, C. / Wu, J.P. / Sun, P.C. / Hu, M.X. / Yan, N.
CitationJournal: Nature / Year: 2014
Title: Crystal structure of the human glucose transporter GLUT1
Authors: Deng, D. / Xu, C. / Sun, P.C. / Wu, J.P. / Yan, C.Y. / Hu, M.X. / Yan, N.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0422
Polymers55,7351
Non-polymers3061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.509, 101.996, 65.604
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Solute carrier family 2, facilitated glucose transporter member 1 / Glucose transporter type 1 / erythrocyte/brain / GLUT-1 / HepG2 glucose transporter


Mass: 55735.133 Da / Num. of mol.: 1 / Mutation: N45T, E329Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A1, GLUT1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11166
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG400, 0.1M MgCl2, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 3.16→40 Å / Num. all: 12834 / Num. obs: 12780 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 88.41 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GC0

4gc0


Resolution: 3.166→32.674 Å / FOM work R set: 0.6827 / SU ML: 0.47 / σ(F): 1.33 / Phase error: 37.38 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 635 4.97 %RANDOM
Rwork0.232 ---
obs0.2343 12780 95.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 288.85 Å2 / Biso mean: 99.25 Å2 / Biso min: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 3.166→32.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 21 0 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093573
X-RAY DIFFRACTIONf_angle_d1.2524850
X-RAY DIFFRACTIONf_chiral_restr0.044571
X-RAY DIFFRACTIONf_plane_restr0.008598
X-RAY DIFFRACTIONf_dihedral_angle_d18.1671277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1656-3.40980.38971220.31122158228086
3.4098-3.75250.30551310.24752511264299
3.7525-4.29440.29061370.22222483262099
4.2944-5.40650.23631310.22132491262298
5.4065-32.67530.26661140.22362502261696
Refinement TLS params.Method: refined / Origin x: 583.8383 Å / Origin y: -31.0884 Å / Origin z: 202.8414 Å
111213212223313233
T0.5424 Å2-0.0227 Å20.1025 Å2-0.5349 Å20.0372 Å2--0.6599 Å2
L3.3068 °20.0108 °20.0876 °2-3.2016 °20.9075 °2--2.3704 °2
S0.0379 Å °-0.2773 Å °0.3084 Å °0.3977 Å °-0.0473 Å °0.1932 Å °-0.1064 Å °-0.1333 Å °-0.0141 Å °
Refinement TLS groupSelection details: ALL

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