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- PDB-6tha: Crystal structure of human sugar transporter GLUT1 (SLC2A1) in th... -

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Basic information

Entry
Database: PDB / ID: 6tha
TitleCrystal structure of human sugar transporter GLUT1 (SLC2A1) in the inward conformation
ComponentsSolute carrier family 2, facilitated glucose transporter member 1
KeywordsMEMBRANE PROTEIN / ALPHA-HELICAL PROTEIN / SUGAR TRANSPORT
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 / glucose transmembrane transporter activity / D-glucose transmembrane transporter activity / Cellular hexose transport ...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 / 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 / cellular hyperosmotic response / photoreceptor cell maintenance / 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 / central nervous system development / female pregnancy / Regulation of insulin secretion / caveola / sarcolemma / response to insulin / cerebral cortex development / Z disc / kinase binding / cellular response to mechanical stimulus / : / melanosome / presynapse / midbody / basolateral plasma membrane / protein-containing complex assembly / blood microparticle / response to hypoxia / apical plasma membrane / Golgi membrane / extracellular exosome / membrane / identical protein binding / 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. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
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 / molecular replacement / Resolution: 2.4 Å
AuthorsPedersen, B.P. / Paulsen, P.A. / Custodio, T.F.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-00052 Denmark
European Research Council637372 Denmark
Other privateCF17-0180 Denmark
CitationJournal: Life Sci Alliance / Year: 2021
Title: Structural comparison of GLUT1 to GLUT3 reveal transport regulation mechanism in sugar porter family.
Authors: Custodio, T.F. / Paulsen, P.A. / Frain, K.M. / Pedersen, B.P.
History
DepositionNov 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_refine_tls / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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
A: Solute carrier family 2, facilitated glucose transporter member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5675
Polymers54,5921
Non-polymers9754
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-4 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.000, 102.180, 69.000
Angle α, β, γ (deg.)90.000, 98.890, 90.000
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: 54591.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A1, GLUT1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop
Details: 42-46 % polyethylene glycol 400, 100-200 mM MgCl2 and 100 mM Mops pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.4→41.656 Å / Num. obs: 32166 / % possible obs: 99.9 % / Redundancy: 7.145 % / Biso Wilson estimate: 78.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.123 / Χ2: 1.163 / Net I/σ(I): 7.2 / Num. measured all: 229827 / Scaling rejects: 993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.57.6112.2180.7236660.4442.38100
2.5-2.67.6061.5611.0231520.6561.675100
2.6-2.77.5481.2331.3426890.7661.324100
2.7-2.87.530.9281.8223580.8430.99799.9
2.8-2.97.5340.6652.5320080.9250.715100
2.9-37.50.5043.3617750.9530.54199.7
3-3.27.4270.3814.5428620.9670.41100
3.2-3.47.3660.2766.5222710.9810.298100
3.4-3.67.2280.1899.7217950.990.20399.7
3.6-3.87.2960.15312.114280.9930.164100
3.8-47.1020.12414.3211470.9950.13399.8
4-57.0730.09518.2434240.9950.103100
5-66.9720.08419.7215090.9960.09199.9
6-83.5290.02816.5811950.9990.03398.6
8-103.3410.02217.624400.9990.02799.1
10-153.3760.02118.083140.9990.02598.1
15-203.5190.02618.74810.9940.03197.6
20-41.6563.1350.02717.59520.9980.03383.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev-2614refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PYP

4pyp


Resolution: 2.4→41.656 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1582 4.93 %
Rwork0.2044 30535 -
obs0.2057 32117 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.76 Å2 / Biso mean: 105.9745 Å2 / Biso min: 57.33 Å2
Refinement stepCycle: final / Resolution: 2.4→41.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 65 13 3556
Biso mean--114.09 91.84 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043624
X-RAY DIFFRACTIONf_angle_d0.654908
X-RAY DIFFRACTIONf_chiral_restr0.04577
X-RAY DIFFRACTIONf_plane_restr0.004600
X-RAY DIFFRACTIONf_dihedral_angle_d22.5331316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4001-2.47750.52881410.50092742100
2.4775-2.56610.49611460.41582780100
2.5661-2.66880.38741420.34732731100
2.6688-2.79020.3291440.29752784100
2.7902-2.93730.30351430.23782762100
2.9373-3.12130.24151340.19212786100
3.1213-3.36220.23091570.18322764100
3.3622-3.70030.21331450.17122772100
3.7003-4.23530.21931540.17392785100
4.2353-5.33430.17681490.18382806100
5.3343-41.6560.21861270.2039282399
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)Origin x (Å)Origin y (Å)Origin z (Å)
14.1531-0.8142-0.04944.35441.3023.31840.12610.0143-0.18520.161-0.24980.13250.1237-0.1070.12770.8063-0.0580.14330.77860.08610.533911.97845.97014.6604
24.23990.8786-1.97352.15590.18942.50090.6043-0.95670.91811.0376-0.23340.1792-0.68620.0438-0.36431.64880.04880.13861.2133-0.1151.37126.870573.63816.0108
33.2114-0.3399-0.22625.9901-0.47352.6569-0.1593-0.45690.27211.10510.3034-1.23240.05860.3675-0.1110.80830.0489-0.16580.90710.01110.705231.826849.049112.8949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 206 )A9 - 206
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 265 )A207 - 265
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 455 )A266 - 455

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