8VT9

WT SthK in the presence of PIP2 and cAMP

PDB DOI: https://doi.org/10.2210/pdb8VT9/pdb
EM Map EMD-43520: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Spirochaeta thermophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-01-26 Released: 2024-09-25
Deposition Author(s): Schmidpeter, P.A.M., Thon, O., Nimigean, C.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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

PubMed: 39300080 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 232.02 kDa
Atom Count: 14,012
Modelled Residue Count: 1,624
Deposited Residue Count: 1,824
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, Crp/Fnr family	A, B, C, D	456	Spirochaeta thermophila	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0GA88
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT5 (Subject of Investigation/LOI) Query on PT5 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth D] SDF format, chain O [auth B] SDF format, chain X [auth C] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C]	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		Interactions Focus chain F [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain F [auth A] Focus chain GA [auth D] Focus chain O [auth B] Focus chain X [auth C]
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CMP Query on CMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth D] SDF format, chain N [auth B] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain W [auth C] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain W [auth C]	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		Interactions Focus chain E [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth D] Focus chain N [auth B] Focus chain W [auth C]