+Open data
-Basic information
Entry | Database: PDB / ID: 8ofi | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Ivabradine bound to HCN4 channel | |||||||||||||||||||||
Components | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / HCN channels / ivabradine / ion transport / drug / hearth / hcn4 | |||||||||||||||||||||
Function / homology | : Function and homology information | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
Authors | Saponaro, A. / Chaves-Sanjuan, A. / Sharifzadeh, A.S. / Clarke, O.B. / Marabelli, C. / Bolognesi, M. / Thiel, G. / Moroni, A. | |||||||||||||||||||||
Funding support | France, Italy, European Union, United States, 6items
| |||||||||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structural determinants of ivabradine block of the open pore of HCN4. Authors: Andrea Saponaro / Jan H Krumbach / Antonio Chaves-Sanjuan / Atiyeh Sadat Sharifzadeh / Alessandro Porro / Roberta Castelli / Kay Hamacher / Martino Bolognesi / Dario DiFrancesco / Oliver B ...Authors: Andrea Saponaro / Jan H Krumbach / Antonio Chaves-Sanjuan / Atiyeh Sadat Sharifzadeh / Alessandro Porro / Roberta Castelli / Kay Hamacher / Martino Bolognesi / Dario DiFrancesco / Oliver B Clarke / Gerhard Thiel / Anna Moroni / Abstract: HCN1-4 channels are the molecular determinants of the I/I current that crucially regulates cardiac and neuronal cell excitability. HCN dysfunctions lead to sinoatrial block (HCN4), epilepsy (HCN1), ...HCN1-4 channels are the molecular determinants of the I/I current that crucially regulates cardiac and neuronal cell excitability. HCN dysfunctions lead to sinoatrial block (HCN4), epilepsy (HCN1), and chronic pain (HCN2), widespread medical conditions awaiting subtype-specific treatments. Here, we address the problem by solving the cryo-EM structure of HCN4 in complex with ivabradine, to date the only HCN-specific drug on the market. Our data show ivabradine bound inside the open pore at 3 Å resolution. The structure unambiguously proves that Y507 and I511 on S6 are the molecular determinants of ivabradine binding to the inner cavity, while F510, pointing outside the pore, indirectly contributes to the block by controlling Y507. Cysteine 479, unique to the HCN selectivity filter (SF), accelerates the kinetics of block. Molecular dynamics simulations further reveal that ivabradine blocks the permeating ion inside the SF by electrostatic repulsion, a mechanism previously proposed for quaternary ammonium ions. | |||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ofi.cif.gz | 352.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ofi.ent.gz | 272.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ofi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ofi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ofi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ofi_validation.xml.gz | 69.2 KB | Display | |
Data in CIF | 8ofi_validation.cif.gz | 100.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/8ofi ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofi | HTTPS FTP |
-Related structure data
Related structure data | 16860MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 98522.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: HCN4, HAC4 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #2: Chemical | ChemComp-VNZ / | Mass: 468.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N2O5 / Feature type: SUBJECT OF INVESTIGATION Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: HCN4 / Type: COMPLEX / Details: HCN4 / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Buffer component | Conc.: 200 mM / Name: sodium chloride / Formula: NaCl |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 30mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 302 K |
-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 / Nominal magnification: 105000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.7 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31670 |
Image scans | Width: 6000 / Height: 4000 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89136 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7NMN Accession code: 7NMN / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|