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- PDB-9oxl: SthK closed state at low temperature, cAMP-bound in the presence ... -

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Basic information

Entry
Database: PDB / ID: 9oxl
TitleSthK closed state at low temperature, cAMP-bound in the presence of DOPE
ComponentsTranscriptional regulator, Crp/Fnr family
KeywordsTRANSPORT PROTEIN / cyclic nucleotide-gated channel / lipid modulation / pacemaker channel / potassium channel / thermoreceptor
Function / homology
Function and homology information


intracellularly cyclic nucleotide-activated monoatomic cation channel activity / protein-containing complex binding / membrane
Similarity search - Function
: / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...: / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Transcriptional regulator, Crp/Fnr family
Similarity search - Component
Biological speciesSpirochaeta thermophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsLi, C.-C. / Nimigean, C.M.
Funding support United States, Taiwan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124451 United States
Ministry of Science and Technology (MoST, Taiwan)111-2917-I-564-001 Taiwan
CitationJournal: Nat Commun / Year: 2026
Title: Mechanism of lipid-dependent cold sensitivity in a model ion channel.
Authors: Chieh-Chin Li / Crina M Nimigean /
Abstract: Temperature sensing enables organisms to detect and respond to environmental changes. While temperature-responsive ion channels are key to this process, the physico-chemical mechanisms by which they ...Temperature sensing enables organisms to detect and respond to environmental changes. While temperature-responsive ion channels are key to this process, the physico-chemical mechanisms by which they sense temperature remain poorly understood. Here, we investigate the molecular details of temperature sensing in the model bacterial channel, SthK from Spirochaeta thermophila. We show that SthK is cold sensitive, displaying higher activity below 30 °C. Remarkably, SthK cold sensitivity depends strongly on membrane lipids, being sensitive in amine-containing lipids but insensitive in anionic lipids. Combining cryo-EM structural analysis, mutagenesis, and functional assays, we identify an intersubunit salt bridge that acts as temperature sensor. This salt bridge forms only in closed states, and determines channel opening by controlling closed-state stability. Lower temperatures weaken salt-bridge interactions, favoring channel opening, and lipid headgroups tune temperature sensitivity by modulating salt-bridge strength. These findings highlight how thermosensitivity can emerge from cooperative interactions between protein and the surrounding membrane.
History
DepositionJun 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, Crp/Fnr family
B: Transcriptional regulator, Crp/Fnr family
C: Transcriptional regulator, Crp/Fnr family
D: Transcriptional regulator, Crp/Fnr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,62436
Polymers204,4744
Non-polymers22,15032
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transcriptional regulator, Crp/Fnr family


Mass: 51118.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Gene: Spith_0644 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: G0GA88
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tetrameric SthK protein / Type: COMPLEX
Details: SthK in complex with cAMP reconstituted into MSP1E3 nanodiscs containing DOPE
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Spirochaeta thermophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41 (DE3)
Buffer solutionpH: 7.4
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 48.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7particle selection
2Leginonimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8model fitting
9PHENIX1.20.1_4487model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1383889
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79604 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01213544
ELECTRON MICROSCOPYf_angle_d1.17118296
ELECTRON MICROSCOPYf_dihedral_angle_d13.9845176
ELECTRON MICROSCOPYf_chiral_restr0.0482120
ELECTRON MICROSCOPYf_plane_restr0.0052196

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