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Yorodumi- EMDB-7484: Structure of the SthK cyclic nucleotide-gated potassium channel i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7484 | |||||||||
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Title | Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP | |||||||||
Map data | nucleotide-gated potassium channel in complex with cAMP, primary map | |||||||||
Sample |
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Keywords | ion channel / lipid / tetramer / cAMP / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / cGMP binding / protein-containing complex binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Spirochaeta thermophila DSM 6578 (bacteria) / Spirochaeta thermophila (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Nimigean CM / Rheinberger J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7484.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-7484-v30.xml emd-7484.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7484_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_7484.png | 89.4 KB | ||
Filedesc metadata | emd-7484.cif.gz | 5.6 KB | ||
Others | emd_7484_additional.map.gz | 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7484 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7484 | HTTPS FTP |
-Validation report
Summary document | emd_7484_validation.pdf.gz | 567.3 KB | Display | EMDB validaton report |
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Full document | emd_7484_full_validation.pdf.gz | 566.9 KB | Display | |
Data in XML | emd_7484_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | emd_7484_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7484 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7484 | HTTPS FTP |
-Related structure data
Related structure data | 6cjuMC 7482C 7483C 6cjqC 6cjtC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7484.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | nucleotide-gated potassium channel in complex with cAMP, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Structure of the SthK cyclic nucleotide-gated potassium channel...
File | emd_7484_additional.map | ||||||||||||
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Annotation | Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP, additional volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of the SthK cyclic nucleotide-gated potassium channel i...
Entire | Name: Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP |
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Components |
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-Supramolecule #1: Structure of the SthK cyclic nucleotide-gated potassium channel i...
Supramolecule | Name: Structure of the SthK cyclic nucleotide-gated potassium channel in complex with cAMP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Spirochaeta thermophila DSM 6578 (bacteria) |
-Macromolecule #1: SthK cyclic nucleotide-gated potassium channel
Macromolecule | Name: SthK cyclic nucleotide-gated potassium channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Spirochaeta thermophila (bacteria) / Strain: ATCC 700085 / DSM 6578 / Z-1203 |
Molecular weight | Theoretical: 51.118574 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAKDIGINSD PNSSSVDKLM KSSGVSNPTY TLVWKVWILA VTLYYAIRIP LTLVFPSLFS PLLPLDILAS LALIADIPLD LAFESRRTS GRKPTLLAPS RLPDLLAALP LDLLVFALHL PSPLSLLSLV RLLKLISVQR SATRILSYRI NPALLRLLSL V GFILLAAH ...String: MAKDIGINSD PNSSSVDKLM KSSGVSNPTY TLVWKVWILA VTLYYAIRIP LTLVFPSLFS PLLPLDILAS LALIADIPLD LAFESRRTS GRKPTLLAPS RLPDLLAALP LDLLVFALHL PSPLSLLSLV RLLKLISVQR SATRILSYRI NPALLRLLSL V GFILLAAH GIACGWMSLQ PPSENPAGTR YLSAFYWTIT TLTTIGYGDI TPSTPTQTVY TIVIELLGAA MYGLVIGNIA SL VSKLDAA KLLHRERVER VTAFLSYKRI SPELQRRIIE YFDYLWETRR GYEEREVLKE LPHPLRLAVA MEIHGDVIEK VPL FKGAGE EFIRDIILHL EPVIYGPGEY IIRAGEMGSD VYFINRGSVE VLSADEKTRY AILSEGQFFG EMALILRAPR TATV RARAF CDLYRLDKET FDRILSRYPE IAAQIQELAV RRKELESSGL VPRGSVKHHH H UniProtKB: Transcriptional regulator, Crp/Fnr family |
-Macromolecule #2: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Macromolecule | Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CMP |
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Molecular weight | Theoretical: 329.206 Da |
Chemical component information | ChemComp-CMP: |
-Macromolecule #3: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
Macromolecule | Name: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 32 / Formula: PGW |
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Molecular weight | Theoretical: 749.007 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |