7VSI

Structure of human SGLT2-MAP17 complex bound with empagliflozin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of inhibition of the human SGLT2-MAP17 glucose transporter.

Niu, Y.Liu, R.Guan, C.Zhang, Y.Chen, Z.Hoerer, S.Nar, H.Chen, L.

(2022) Nature 601: 280-284

  • DOI: https://doi.org/10.1038/s41586-021-04212-9
  • Primary Citation of Related Structures:  
    7VSI

  • PubMed Abstract: 

    Human sodium-glucose cotransporter 2 (hSGLT2) mediates the reabsorption of the majority of filtrated glucose in the kidney 1 . Pharmacological inhibition of hSGLT2 by oral small-molecule inhibitors, such as empagliflozin, leads to enhanced excretion of glucose and is widely used in the clinic to manage blood glucose levels for the treatment of type 2 diabetes 1 . Here we determined the cryogenic electron microscopy structure of the hSGLT2-MAP17 complex in the empagliflozin-bound state to an overall resolution of 2.95 Å. Our structure shows eukaryotic SGLT-specific structural features. MAP17 interacts with transmembrane helix 13 of hSGLT2. Empagliflozin occupies both the sugar-substrate-binding site and the external vestibule to lock hSGLT2 in an outward-open conformation, thus inhibiting the transport cycle. Our work provides a framework for understanding the mechanism of SLC5A family glucose transporters and also develops a foundation for the future rational design and optimization of new inhibitors targeting these transporters.


  • Organizational Affiliation

    Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/glucose cotransporter 2672Homo sapiensMutation(s): 0 
Gene Names: SLC5A2SGLT2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P31639 (Homo sapiens)
Explore P31639 
Go to UniProtKB:  P31639
GTEx:  ENSG00000140675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31639
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PDZK1-interacting protein 156Homo sapiensMutation(s): 0 
Gene Names: PDZK1IP1MAP17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13113 (Homo sapiens)
Explore Q13113 
Go to UniProtKB:  Q13113
GTEx:  ENSG00000162366 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13113
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7R3 (Subject of Investigation/LOI)
Query on 7R3

Download Ideal Coordinates CCD File 
E [auth A](2S,3R,4R,5S,6R)-2-[4-chloranyl-3-[[4-[(3S)-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol
C23 H27 Cl O7
OBWASQILIWPZMG-QZMOQZSNSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91957201
National Natural Science Foundation of China (NSFC)China31821091
National Natural Science Foundation of China (NSFC)China31870833

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2022-02-16
    Changes: Database references