+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16860 | |||||||||||||||||||||
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Title | Ivabradine bound to HCN4 channel | |||||||||||||||||||||
Map data | sharped map | |||||||||||||||||||||
Sample |
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Keywords | HCN channels / ivabradine / ion transport / MEMBRANE PROTEIN / drug / hearth / hcn4 | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
Authors | Saponaro A / Chaves-Sanjuan A / Sharifzadeh AS / Clarke OB / Marabelli C / Bolognesi M / Thiel G / Moroni A | |||||||||||||||||||||
Funding support | France, Italy, European Union, United States, 6 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16860.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-16860-v30.xml emd-16860.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16860_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_16860.png | 170.8 KB | ||
Masks | emd_16860_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-16860.cif.gz | 7 KB | ||
Others | emd_16860_additional_1.map.gz emd_16860_half_map_1.map.gz emd_16860_half_map_2.map.gz | 120.3 MB 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16860 | HTTPS FTP |
-Validation report
Summary document | emd_16860_validation.pdf.gz | 910.6 KB | Display | EMDB validaton report |
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Full document | emd_16860_full_validation.pdf.gz | 910.2 KB | Display | |
Data in XML | emd_16860_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_16860_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16860 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16860 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16860.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharped map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16860_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharped map
File | emd_16860_additional_1.map | ||||||||||||
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Annotation | unsharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half a
File | emd_16860_half_map_1.map | ||||||||||||
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Annotation | half a | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half b
File | emd_16860_half_map_2.map | ||||||||||||
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Annotation | half b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HCN4
Entire | Name: HCN4 |
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Components |
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-Supramolecule #1: HCN4
Supramolecule | Name: HCN4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: HCN4 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...
Macromolecule | Name: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 98.522727 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDKLPPSMRK RLYSLPQQVG AKAWIMDEEE DAEEEGAGGR QDPRRRSIRL RPLPSPSPSP SAAAAAAGGA ESRGAALGGA ADGEGPARG AAKSSTNGDC RRFRGSLASL GSRGGGGGGG STGGGSHGHL HDSAEERRLI AEGDASPGED RTPPGLAAEP E RPGAPAPP ...String: MDKLPPSMRK RLYSLPQQVG AKAWIMDEEE DAEEEGAGGR QDPRRRSIRL RPLPSPSPSP SAAAAAAGGA ESRGAALGGA ADGEGPARG AAKSSTNGDC RRFRGSLASL GSRGGGGGGG STGGGSHGHL HDSAEERRLI AEGDASPGED RTPPGLAAEP E RPGAPAPP AASPPQVPSS CGEQRPADAA VKVEGGAAAG DQILPEAEAR LGQAGFMQRQ FGAMLQPGVN KFSLRMFGSQ KA VEREQER VKSAGFWIIH PYSDFRFYWD LTMLLLMVGN LIIIPVGITF FKDENTTPWI VFNVVSDTFF LIDLVLNFRT GIV VEDNTD IILDPRRIKM KYLKSWFVVD FVSSIPVDYI FLIVETRIDS EVYKTARALR IVRFTKILSL LRLLRLSRLI RYIH QWEEI FHMTYDLASA VVRIVNLIGM MLLLCHWDGC LQFLVPMLQD FPDDCWVSLN NMVNNSWGKQ YSYALFKAMS HMLCI GYGR QAPMGMSDVW LTMLSMIVGA TCYAMFIGHA TALIQSLDSS RRQYQEKYKQ VEQYMSFHKL PPDTRQRIHD YYEHRY QGK MFDEESILGE LSEPLREEII NFNCRKLVAS MPLFANADPN FVTSMLTKLR FEVFQPGDYI IREGTIGKKM YFIQHGV VS VLTKGNKETK LADGSYFGEI CLLTRGRRTA SVRADTYCRL YSLSVDNFNE VLEEYPMMRR AFETVALDRL DRIGKKNS I HKVQHDLSSG VSNYQENAIV QRIVQHDREM AHCARRAQAT TPVAPAIWTP LIQAPLQAAA QDLKLISASQ PALPQDGAQ TLRRASPHSS SGESVAALPP AGGPFPRAPG RPPGAGPGQH VTLTLPRKAS SGSLPPPLSL FGPRAAPRLT AAPQREPGAK SEPVRSKLP SNL |
-Macromolecule #2: Ivabradine
Macromolecule | Name: Ivabradine / type: ligand / ID: 2 / Number of copies: 1 / Formula: VNZ |
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Molecular weight | Theoretical: 468.585 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7 / Component - Concentration: 200.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride |
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 302 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 31670 / Average exposure time: 1.7 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |