8VT9

WT SthK in the presence of PIP2 and cAMP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

PIP2 inhibits pore opening of the cyclic nucleotide-gated channel SthK.

Thon, O.Wang, Z.Schmidpeter, P.A.M.Nimigean, C.M.

(2024) Nat Commun 15: 8230-8230

  • DOI: https://doi.org/10.1038/s41467-024-52469-1
  • Primary Citation of Related Structures:  
    8VT9, 8VTA, 8VTB

  • PubMed Abstract: 

    The signaling lipid phosphatidylinositol-4,5-bisphosphate (PIP2) regulates many ion channels. It inhibits eukaryotic cyclic nucleotide-gated (CNG) channels while activating their relatives, the hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels. The prokaryotic SthK channel from Spirochaeta thermophila shares features with CNG and HCN channels and is an established model for this channel family. Here, we show SthK activity is inhibited by PIP2. A cryo-EM structure of SthK in nanodiscs reveals a PIP2-fitting density coordinated by arginine and lysine residues from the S4 helix and the C-linker, located between voltage-sensing and pore domains of adjacent subunits. Mutation of two arginine residues weakens PIP2 inhibition with the double mutant displaying insensitivity to PIP2. We propose that PIP2 inhibits SthK by gluing S4 and S6 together, stabilizing a resting channel conformation. The PIP2 binding site is partially conserved in CNG channels suggesting the possibility of a similar inhibition mechanism in the eukaryotic homologs.


  • Organizational Affiliation

    Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, Crp/Fnr family
A, B, C, D
456Spirochaeta thermophilaMutation(s): 0 
Gene Names: Spith_0644
Membrane Entity: Yes 
UniProt
Find proteins for G0GA88 (Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203))
Explore G0GA88 
Go to UniProtKB:  G0GA88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0GA88
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT5 (Subject of Investigation/LOI)
Query on PT5

Download Ideal Coordinates CCD File 
F [auth A],
GA [auth D],
O [auth B],
X [auth C]
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-HJBQCNPJSA-N
PCW
Query on PCW

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
NA [auth D],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Y [auth C],
Z [auth C]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CMP
Query on CMP

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth D],
N [auth B],
W [auth C]
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

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 StatesGM124451

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references