7TJ6

SthK open state, cAMP-bound in the presence of POPA


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Anionic lipids unlock the gates of select ion channels in the pacemaker family.

Schmidpeter, P.A.M.Wu, D.Rheinberger, J.Riegelhaupt, P.M.Tang, H.Robinson, C.V.Nimigean, C.M.

(2022) Nat Struct Mol Biol 29: 1092-1100

  • DOI: https://doi.org/10.1038/s41594-022-00851-2
  • Primary Citation of Related Structures:  
    7TJ5, 7TJ6, 7TKT

  • PubMed Abstract: 

    Lipids play important roles in regulating membrane protein function, but the molecular mechanisms used are elusive. Here we investigated how anionic lipids modulate SthK, a bacterial pacemaker channel homolog, and HCN2, whose activity contributes to pacemaking in the heart and brain. Using SthK allowed the reconstitution of purified channels in controlled lipid compositions for functional and structural assays that are not available for the eukaryotic channels. We identified anionic lipids bound tightly to SthK and their exact binding locations and determined that they potentiate channel activity. Cryo-EM structures in the most potentiating lipids revealed an open state and identified a nonannular lipid bound with its headgroup near an intersubunit salt bridge that clamps the intracellular channel gate shut. Breaking this conserved salt bridge abolished lipid modulation in SthK and eukaryotic HCN2 channels, indicating that anionic membrane lipids facilitate channel opening by destabilizing these interactions. Our findings underline the importance of state-dependent protein-lipid interactions.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transcriptional regulator, Crp/Fnr family
A, B, C, D
456Spirochaeta thermophila DSM 6578Mutation(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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D21 (Subject of Investigation/LOI)
Query on D21

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth D]
(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
C37 H71 O8 P
OPVZUEPSMJNLOM-PGUFJCEWSA-N
CMP
Query on CMP

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
S [auth C],
Z [auth D]
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
RECONSTRUCTIONRELION3.1.3

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 StatesR01GM124451
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM088352
American Heart AssociationUnited States18POST33960309

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Refinement description