[English] 日本語
Yorodumi
- EMDB-61099: Cryo-EM structure of the human glucose transporter, GLUT7 in outw... -

+
Open data


ID or keywords:

Loading...

-
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


monosaccharide transmembrane transport / hexose transmembrane transporter activity / sugar transmembrane transporter activity / fructose transmembrane transporter activity / fructose transmembrane transport / hexose transmembrane transport / Cellular hexose transport / D-glucose transmembrane transporter activity / 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. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / 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

-
Structure visualization

Supplemental images

emd_61099.png

Downloads & links

-
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)

Slices (1/2)

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 °

-
Supplemental data

-
Half map: #2

Fileemd_61099_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61099_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more