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- EMDB-7484: Structure of the SthK cyclic nucleotide-gated potassium channel i... -

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Basic information

Entry
Database: EMDB / ID: 7484
TitleStructure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP
Map datanucleotide-gated potassium channel in complex with cAMP, primary map
SampleStructure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP
  • SthK cyclic nucleotide-gated potassium channel
  • (ligand) x 2
Function / homologyCyclic nucleotide-binding domain / Potassium channel domain / RmlC-like jelly roll fold / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding domain / Ion channel / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding domain signature 2. / cAMP/cGMP binding motif profile. ...Cyclic nucleotide-binding domain / Potassium channel domain / RmlC-like jelly roll fold / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-binding-like / Cyclic nucleotide-binding domain / Ion channel / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding domain signature 2. / cAMP/cGMP binding motif profile. / integral component of membrane / Putative transcriptional regulator, Crp/Fnr family
Function and homology information
SourceSpirochaeta thermophila DSM 6578 (bacteria) / Spirochaeta thermophila (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsNimigean CM / Rheinberger J
CitationJournal: Elife / Year: 2018
Title: Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures.
Authors: Jan Rheinberger / Xiaolong Gao / Philipp Am Schmidpeter / Crina M Nimigean
Abstract: Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different ...Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the 'resting' and 'activated' structures suggest a mechanism for ligand discrimination.
Validation ReportPDB-ID: 6cju

SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Aug 1, 2018 / Last update: Aug 1, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cju
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7484.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.07 Å/pix.
= 274.752 Å
256 pix
1.07 Å/pix.
= 274.752 Å
256 pix
1.07 Å/pix.
= 274.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07325 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.22500744 - 0.39263234
Average (Standard dev.)0.00054005807 (0.010498776)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 274.752 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z274.752274.752274.752
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2250.3930.001

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Supplemental data

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Sample components

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Entire Structure of the SthK cyclic nucleotide-gated potassium channel i...

EntireName: Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP
Number of components: 4

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Component #1: protein, Structure of the SthK cyclic nucleotide-gated potassium ...

ProteinName: Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP
Recombinant expression: No
SourceSpecies: Spirochaeta thermophila DSM 6578 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, SthK cyclic nucleotide-gated potassium channel

ProteinName: SthK cyclic nucleotide-gated potassium channel / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 51.118574 kDa
SourceSpecies: Spirochaeta thermophila (bacteria) / Strain: ATCC 700085 / DSM 6578 / Z-1203
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

LigandName: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.329206 kDa

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Component #4: ligand, (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phos...

LigandName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Number of Copies: 32 / Recombinant expression: No
MassTheoretical: 0.749007 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 72 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 81501
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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