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Yorodumi- EMDB-12513: cAMP-bound rabbit HCN4 stabilized in LMNG-CHS detergent mixture -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12513 | |||||||||||||||||||||
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Title | cAMP-bound rabbit HCN4 stabilized in LMNG-CHS detergent mixture | |||||||||||||||||||||
Map data | sharped map | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information intracellularly cAMP-activated cation channel activity / sodium channel activity / monoatomic ion channel complex / voltage-gated potassium channel activity / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / regulation of heart rate / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Giese H / Chaves-Sanjuan A / Saponaro A / Clarke O / Bolognesi M / Mancia F / Hendrickson WA / Thiel G / Santoro B / Moroni A | |||||||||||||||||||||
Funding support | United States, Italy, European Union, 6 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Gating movements and ion permeation in HCN4 pacemaker channels. Authors: Andrea Saponaro / Daniel Bauer / M Hunter Giese / Paolo Swuec / Alessandro Porro / Federica Gasparri / Atiyeh Sadat Sharifzadeh / Antonio Chaves-Sanjuan / Laura Alberio / Giacomo Parisi / ...Authors: Andrea Saponaro / Daniel Bauer / M Hunter Giese / Paolo Swuec / Alessandro Porro / Federica Gasparri / Atiyeh Sadat Sharifzadeh / Antonio Chaves-Sanjuan / Laura Alberio / Giacomo Parisi / Gabriele Cerutti / Oliver B Clarke / Kay Hamacher / Henry M Colecraft / Filippo Mancia / Wayne A Hendrickson / Steven A Siegelbaum / Dario DiFrancesco / Martino Bolognesi / Gerhard Thiel / Bina Santoro / Anna Moroni / Abstract: The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current I/I that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy ...The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current I/I that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy (cryo-EM) structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures sheds light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlights the regulatory role of a Mg coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K/Na permeation. Our results contribute mechanistic understanding on HCN channel gating, cyclic nucleotide-dependent modulation, and ion permeation. | |||||||||||||||||||||
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_12513.map.gz | 71 MB | EMDB map data format | |
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Header (meta data) | emd-12513-v30.xml emd-12513.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12513_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_12513.png | 233.1 KB | ||
Masks | emd_12513_msk_1.map | 76.8 MB | Mask map | |
Others | emd_12513_additional_1.map.gz emd_12513_half_map_1.map.gz emd_12513_half_map_2.map.gz | 38 MB 70.6 MB 70.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12513 | HTTPS FTP |
-Related structure data
Related structure data | 7np4MC 7nmnC 7np3C M: atomic model generated by this map C: citing same article (ref.) |
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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_12513.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharped map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12513_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: unsharped map
File | emd_12513_additional_1.map | ||||||||||||
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Annotation | unsharped map | ||||||||||||
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Density Histograms |
-Half map: half 1
File | emd_12513_half_map_1.map | ||||||||||||
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Annotation | half 1 | ||||||||||||
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Density Histograms |
-Half map: half 2
File | emd_12513_half_map_2.map | ||||||||||||
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Annotation | half 2 | ||||||||||||
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) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...
Macromolecule | Name: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4,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: 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: |
-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: NaClSodium chloride / Component - Name: sodium chloride |
Grid | Model: Quantifoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.85 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |