8QUD

Cryo-EM Structure of Human Kv3.1 in Complex with Modulator AUT5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The binding and mechanism of a positive allosteric modulator of Kv3 channels.

Liang, Q.Chi, G.Cirqueira, L.Zhi, L.Marasco, A.Pilati, N.Gunthorpe, M.J.Alvaro, G.Large, C.H.Sauer, D.B.Treptow, W.Covarrubias, M.

(2024) Nat Commun 15: 2533-2533

  • DOI: https://doi.org/10.1038/s41467-024-46813-8
  • Primary Citation of Related Structures:  
    8QUC, 8QUD

  • PubMed Abstract: 

    Small-molecule modulators of diverse voltage-gated K + (Kv) channels may help treat a wide range of neurological disorders. However, developing effective modulators requires understanding of their mechanism of action. We apply an orthogonal approach to elucidate the mechanism of action of an imidazolidinedione derivative (AUT5), a highly selective positive allosteric modulator of Kv3.1 and Kv3.2 channels. AUT5 modulation involves positive cooperativity and preferential stabilization of the open state. The cryo-EM structure of the Kv3.1/AUT5 complex at a resolution of 2.5 Å reveals four equivalent AUT5 binding sites at the extracellular inter-subunit interface between the voltage-sensing and pore domains of the channel's tetrameric assembly. Furthermore, we show that the unique extracellular turret regions of Kv3.1 and Kv3.2 essentially govern the selective positive modulation by AUT5. High-resolution apo and bound structures of Kv3.1 demonstrate how AUT5 binding promotes turret rearrangements and interactions with the voltage-sensing domain to favor the open conformation.


  • Organizational Affiliation

    Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily C member 1A,
B,
C [auth D],
D [auth C]
518Homo sapiensMutation(s): 1 
Gene Names: KCNC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48547 (Homo sapiens)
Explore P48547 
Go to UniProtKB:  P48547
PHAROS:  P48547
GTEx:  ENSG00000129159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48547
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCF
Query on PCF

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B],
Q [auth D],
U [auth C]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
T [auth D],
X [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
WY0 (Subject of Investigation/LOI)
Query on WY0

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
R [auth D],
V [auth C]
(5R)-5-ethyl-3-(6-spiro[2H-1-benzofuran-3,1'-cyclopropane]-4-yloxypyridin-3-yl)imidazolidine-2,4-dione
C20 H19 N3 O4
XOWFIAMSTPQWIU-CYBMUJFWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
S [auth D],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
P [auth B]
Y [auth C]
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Y [auth C],
Z [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--
Innovative Medicines InitiativeSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release