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- PDB-35vc: cAMP-bound WT SthK in 4:1 DOPC:POPA nanodiscs -

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Basic information

Entry
Database: PDB / ID: 35vc
TitlecAMP-bound WT SthK in 4:1 DOPC:POPA nanodiscs
ComponentsPutative transcriptional regulator, Crp/Fnr family
KeywordsMEMBRANE PROTEIN / ion channel / lipid modulation / phosphatidic acid / allostery / ligand binding
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 / Chem-D21 / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Transcriptional regulator, Crp/Fnr family
Similarity search - Component
Biological speciesWinmispira thermophila DSM 6578 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsNewton, A.N. / Kuforiji, A.E. / Schmidpeter, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM159863 United States
CitationJournal: Nat Commun / Year: 2026
Title: Concentration-dependent switching between ligand-like and solvent-like lipid regulation in a model ion channel
Authors: Newton, A.J. / Kuforiji, A.E. / Schmidpeter, P.A.
History
DepositionMay 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / 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: Putative transcriptional regulator, Crp/Fnr family
B: Putative transcriptional regulator, Crp/Fnr family
C: Putative transcriptional regulator, Crp/Fnr family
D: Putative transcriptional regulator, Crp/Fnr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,23332
Polymers204,4744
Non-polymers19,75928
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative transcriptional regulator, Crp/Fnr family


Mass: 51118.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: fusion of SthK with an N-terminal expression-enhancing peptide and a C-terminal tetra-His tag
Source: (gene. exp.) Winmispira thermophila DSM 6578 (bacteria)
Gene: Spith_0644 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
#3: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#4: Chemical
ChemComp-D21 / (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate


Mass: 674.929 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H71O8P
Has ligand of interestN
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: tetrameric SthK protein in the presence of 3 mM cAMP reconstituted into 4:1 DOPC:POPA nanodiscs
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Spirochaeta thermophila (bacteria) / Strain: DSM 6578
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMPotassium chlorideKCl1
33 mMcAMP1
43 mMfluorinated Fos-choline 81
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: cAMP-bound tetrameric WT SthK in 4:1 DOPC:POPA nanodiscs
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298.15 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: 2700 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 47.11 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12856
EM imaging opticsEnergyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Leginon3.6image acquisition
4CTFFIND4CTF correction
7UCSF ChimeraXmodel fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.21.2_5419model refinement
14Coot0.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1254857
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257548 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6CJU

6cju


Accession code: 6CJU / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313516
ELECTRON MICROSCOPYf_angle_d0.5418248
ELECTRON MICROSCOPYf_dihedral_angle_d14.485308
ELECTRON MICROSCOPYf_chiral_restr0.0382100
ELECTRON MICROSCOPYf_plane_restr0.0042208

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