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- EMDB-61099: Cryo-EM structure of the human glucose transporter, GLUT7 in outw... -

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Basic information

Entry
Database: EMDB / ID: EMD-61099
TitleCryo-EM structure of the human glucose transporter, GLUT7 in outward-facing open conformation
Map data
Sample
  • Organelle or cellular component: human glucose transporter 7, SLC2A7
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHuman glucose transporter 7 / SLC2A7 / Fructose transporter / Intestinal hexose absorption / Membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


hexose transmembrane transporter activity / monosaccharide transmembrane transport / fructose transmembrane transporter activity / sugar transmembrane transporter activity / fructose transmembrane transport / hexose transmembrane transport / D-glucose transmembrane transporter activity / Cellular hexose transport / D-glucose transmembrane transport / apical plasma membrane / plasma membrane
Similarity search - Function
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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLee SS / Kim S / Jin MS
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9I4022846 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1A2C1091278 Korea, Republic Of
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Cryo-EM structure of the human glucose transporter GLUT7.
Authors: Sang Soo Lee / Subin Kim / Mi Sun Jin /
Abstract: GLUT7 is a Class II glucose transporter predominantly expressed at the apical membrane of enterocytes in the small intestine. Here, we report the cryo-EM structure of nanodisc-reconstituted human ...GLUT7 is a Class II glucose transporter predominantly expressed at the apical membrane of enterocytes in the small intestine. Here, we report the cryo-EM structure of nanodisc-reconstituted human GLUT7 in the apo state at 3.3 Å resolution. Our atomic model reveals a typical major facilitator superfamily fold, with the substrate-binding site open to the extracellular side of the membrane. Despite the nearly identical conformation to its closest family member, rat GLUT5, our structure unveils distinct features of the substrate-binding cavity that may influence substrate specificity and binding mode. A homology model of the inward-open human GLUT7 indicates that similar to other members of the GLUT family, it may undergo a global rocker-switch-like reorientation of the transmembrane bundles to facilitate substrate translocation across the membrane. Our work enhances the current structural understanding of the GLUT family, and lays a foundation for rational design of regulators of GLUTs and other sugar transporters.
History
DepositionAug 7, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61099.png

Downloads & links

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Map

FileDownload / File: emd_61099.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 300 pix.
= 172.2 Å		0.57 Å/pix.
x 300 pix.
= 172.2 Å		0.57 Å/pix.
x 300 pix.
= 172.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.574 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.32451326 - 0.6050044
Average (Standard dev.)0.0008429073 (±0.014652633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 172.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61099_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61099_half_map_2.map
Projections & Slices
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Sample components

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Entire : human glucose transporter 7, SLC2A7

EntireName: human glucose transporter 7, SLC2A7
Components
  • Organelle or cellular component: human glucose transporter 7, SLC2A7
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human glucose transporter 7, SLC2A7

SupramoleculeName: human glucose transporter 7, SLC2A7 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 2, facilitated glucose transporter member 7

MacromoleculeName: Solute carrier family 2, facilitated glucose transporter member 7
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.777195 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MENKEAGTPP PIPSREGRLQ PTLLLATLSA AFGSAFQYGY NLSVVNTPHK VFKSFYNETY FERHATFMDG KLMLLLWSCT VSMFPLGGL LGSLLVGLLV DSCGRKGTLL INNIFAIIPA ILMGVSKVAK AFELIVFSRV VLGVCAGISY SALPMYLGEL A PKNLRGMV ...String:
MENKEAGTPP PIPSREGRLQ PTLLLATLSA AFGSAFQYGY NLSVVNTPHK VFKSFYNETY FERHATFMDG KLMLLLWSCT VSMFPLGGL LGSLLVGLLV DSCGRKGTLL INNIFAIIPA ILMGVSKVAK AFELIVFSRV VLGVCAGISY SALPMYLGEL A PKNLRGMV GTMTEVFVIV GVFLAQIFSL QAILGNPAGW PVLLALTGVP ALLQLLTLPF FPESPRYSLI QKGDEATARQ AL RRLRGHT DMEAELEDMR AEARAERAEG HLSVLHLCAL RSLRWQLLSI IVLMAGQQLS GINAINYYAD TIYTSAGVEA AHS QYVTVG SGVVNIVMTI TSAVLVERLG RRHLLLAGYG ICGSACLVLT VVLLFQNRVP ELSYLGIICV FAYIAGHSIG PSPV PSVVR TEIFLQSSRR AAFMVDGAVH WLTNFIIGFL FPSIQEAIGA YSFIIFAGIC LLTAIYIYVV IPETKGKTFV EINRI FAKR NRVKLPEEKE ETIDAGPPTA SPAKETSF

UniProtKB: Solute carrier family 2, facilitated glucose transporter member 7

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112978
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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