Crystal structure of the human glucose transporter GLUT1

Abstract

The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

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Figure 1: Overall structure of the human glucose transporter GLUT1.
Figure 2: Structural mapping of disease-derived mutations in GLUT1.
Figure 3: The ICH domain serves as a latch that tightens the intracellular gate.
Figure 4: Analysis of the extracellular gate of the inward-open GLUT1.
Figure 5: A working model for GLUT1.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The X-ray crystallographic coordinates and structure factor files of human GLUT1(N45T/E329Q) have been deposited in the Protein Data Bank (PDB) with the accession code 4PYP.

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Acknowledgements

We thank J. He, L. Tang, F. Yu and S. Huang at Shanghai Synchrotron Radiation Facility (SSRF). This work was supported by funds from the Ministry of Science and Technology (grant number 2011CB910501), Projects 31321062-20131319400, 31125009 and 91017011 of the National Natural Science Foundation of China, and funds from Tsinghua-Peking Center for Life Sciences. The research of N.Y. was supported in part by an International Early Career Scientist grant from the Howard Hughes Medical Institute.

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N.Y. conceived the project. D.D. and N.Y. designed all experiments. D.D., C.X., P.S., J.W., C.Y. and M.H. performed the experiments. All authors analysed the data and contributed to manuscript preparation. N.Y. wrote the manuscript.

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Correspondence to Nieng Yan.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Structure determination of GLUT1.

a, The 2Fo − Fc electron density map. The stereo-view map for one representative slab, shown as cyan mesh, is contoured at 1.0σ. b, The crystal packing of GLUT1 in the space group C2. Each GLUT1 molecule is shown as rainbow-coloured ribbon, blue and red for the N and C termini, respectively.

Extended Data Figure 2 One β-NG molecule occupies the substrate-binding site of the inward-open GLUT1.

a, The ‘omit’ electron density observed in the inward-open cavity of GLUT1. The electron density, shown as magenta mesh, is contoured at 3.0σ. The N, C and ICH domains are coloured green, blue and yellow, respectively. b, A β-NG molecule fits well into the electron density inside the cavity. The 2Fo − Fc electron density map (cyan mesh) for the β-NG molecule is contoured at 1.0σ. c, The overall GLUT1 structure with the bound β-NG molecule. β-NG is represented by white spheres. d, The coordination of the sugar moiety of β-NG by GLUT1 is similar to the binding of d-glucose by XylE. The structures of GLUT1 (blue) and XylE (cyan) are superimposed relative to their respective C domains. The ligands are shown in stick representation. Despite the similarity between d-glucose and β-NG, we cannot exclude the possibility that presence of the aliphatic tail of β-NG in GLUT1 may subtly affect positioning of the sugar moiety compared to d-glucose. e, Coordination of the d-glucopyranoside of β-NG by GLUT1. The d-glucopyranoside of β-NG is hydrogen-bonded to the surrounding polar residues in the C domain, including Gln 282/Gln 283/Asn 288 from TM7, Asn 317 from TM8, and Asn 415 from TM11. The residues whose mutations are associated with GLUT1 deficiency syndrome are labelled in magenta.

Extended Data Figure 3 Interactions between the N and C domains observed in the inward-open GLUT1 and the outward-facing XylE.

a, In GLUT1, the inter-domain contacts, mainly on the extracellular side, include both van der Waals interactions and hydrogen bonds. Residues whose mutations are associated with GLUT1 deficiency syndrome are labelled in magenta. b, In XylE, there are only limited interactions between the N and C domains at the transmembrane region.

Extended Data Figure 4 Conformational differences between GLUT1 and XylE.

a, Structural comparison of the inward-open GLUT1 and the outward-facing, partly occluded, ligand-bound XylE. Similar intracellular views are shown for GLUT1 and XylE. Note that the C-terminal helix IC5, which was referred to as IC4 in a previous study of XylE (ref. 28), is invisible in the structure of GLUT1 probably due to its inherent flexibility in this conformation. b, c, Structural superimpositions of GLUT1 and XylE relative to their respective N domains (b) and C domains (c). A detailed analysis can be found in Figs 3 and 4. d, Conformational differences of TM7 between GLUT1 and XylE. Compared to that in XylE, the extracellular segment of TM7 in GLUT1 is further bent away from the transport path.

Extended Data Figure 5 Sequence alignment of GLUT1-4 with XylE.

Secondary structural elements of GLUT1 are indicated above the sequence alignment. Invariant and highly conserved amino acids are shaded yellow and grey, respectively. The conserved sugar porter family signature motifs are underscored with red lines. The residues that are hydrogen-bonded to d-glucose in XylE are shaded red. The GLUT1 residues whose mutations were found in GLUT1 deficiency syndrome are indicated by black circles above. The sequences were aligned with ClustalW.

Extended Data Table 1 Statistics of data collection and refinement for GLUT1
Extended Data Table 2 Summary of disease-related sequence variations of GLUT1

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Deng, D., Xu, C., Sun, P. et al. Crystal structure of the human glucose transporter GLUT1. Nature 510, 121–125 (2014). https://doi.org/10.1038/nature13306

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