7M17

SN-407-LRRC8A in MSP1E3D1 lipid nanodiscs (Pose-1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Small molecule SWELL1 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes.

Gunasekar, S.K.Xie, L.Kumar, A.Hong, J.Chheda, P.R.Kang, C.Kern, D.M.My-Ta, C.Maurer, J.Heebink, J.Gerber, E.E.Grzesik, W.J.Elliot-Hudson, M.Zhang, Y.Key, P.Kulkarni, C.A.Beals, J.W.Smith, G.I.Samuel, I.Smith, J.K.Nau, P.Imai, Y.Sheldon, R.D.Taylor, E.B.Lerner, D.J.Norris, A.W.Klein, S.Brohawn, S.G.Kerns, R.Sah, R.

(2022) Nat Commun 13: 784-784

  • DOI: https://doi.org/10.1038/s41467-022-28435-0
  • Primary Citation of Related Structures:  
    7M17, 7M19

  • PubMed Abstract: 

    Type 2 diabetes is associated with insulin resistance, impaired pancreatic β-cell insulin secretion, and nonalcoholic fatty liver disease. Tissue-specific SWELL1 ablation impairs insulin signaling in adipose, skeletal muscle, and endothelium, and impairs β-cell insulin secretion and glycemic control. Here, we show that I Cl,SWELL and SWELL1 protein are reduced in adipose and β-cells in murine and human diabetes. Combining cryo-electron microscopy, molecular docking, medicinal chemistry, and functional studies, we define a structure activity relationship to rationally-design active derivatives of a SWELL1 channel inhibitor (DCPIB/SN-401), that bind the SWELL1 hexameric complex, restore SWELL1 protein, plasma membrane trafficking, signaling, glycemic control and islet insulin secretion via SWELL1-dependent mechanisms. In vivo, SN-401 restores glycemic control, reduces hepatic steatosis/injury, improves insulin-sensitivity and insulin secretion in murine diabetes. These findings demonstrate that SWELL1 channel modulators improve SWELL1-dependent systemic metabolism in Type 2 diabetes, representing a first-in-class therapeutic approach for diabetes and nonalcoholic fatty liver disease.


  • Organizational Affiliation

    Department of Internal Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Volume-regulated anion channel subunit LRRC8A
A, B, C, D, E
A, B, C, D, E, F
819Mus musculusMutation(s): 0 
Gene Names: Lrrc8aLrrc8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q80WG5 (Mus musculus)
Explore Q80WG5 
Go to UniProtKB:  Q80WG5
IMPC:  MGI:2652847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80WG5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth E],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Y [auth F]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
YNJ (Subject of Investigation/LOI)
Query on YNJ

Download Ideal Coordinates CCD File 
N [auth C]7-{[(2S)-2-butyl-6,7-dichloro-2-cyclopentyl-1-oxo-2,3-dihydro-1H-inden-5-yl]oxy}heptanoic acid
C25 H34 Cl2 O4
FIDRMVPJOHBYQH-VWLOTQADSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM128263
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM123496
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States1R01DK106009

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 2.0: 2021-09-29
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2022-02-23
    Changes: Database references