[English] 日本語
Yorodumi- PDB-5v4s: CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v4s | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel | |||||||||||||||
Components | Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein | |||||||||||||||
Keywords | TRANSPORT PROTEIN / Ion channel / cyclic nucleotide / allostery / vision / olfaction | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Leptospira licerasiae serovar Varillal str. VAR 010 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | James, Z.M. / Borst, A.J. / Haitin, Y. / Frenz, B. / DiMaio, F. / Zagotta, W.N. / Veesler, D. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Authors: Zachary M James / Andrew J Borst / Yoni Haitin / Brandon Frenz / Frank DiMaio / William N Zagotta / David Veesler / Abstract: Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. ...Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from -which shares sequence similarity to eukaryotic CNG and HCN channels-in the presence of a saturating concentration of cAMP. A short S4-S5 linker connects nearby voltage-sensing and pore domains to produce a non-domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5v4s.cif.gz | 275.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5v4s.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 5v4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v4s_validation.pdf.gz | 774.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5v4s_full_validation.pdf.gz | 780.2 KB | Display | |
Data in XML | 5v4s_validation.xml.gz | 41 KB | Display | |
Data in CIF | 5v4s_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/5v4s ftp://data.pdbj.org/pub/pdb/validation_reports/v4/5v4s | HTTPS FTP |
-Related structure data
Related structure data | 8632MC 8633MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 53464.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira licerasiae serovar Varillal str. VAR 010 (bacteria) Gene: LEP1GSC185_1946 / Production host: Escherichia coli (E. coli) / References: UniProt: I0XVQ9 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: LliK / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.2 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Leptospira licerasiae serovar Varillal str. VAR 010 (bacteria) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 379000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18737 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |