[English] 日本語
Yorodumi- EMDB-0094: Structure of human HCN4 hyperpolarization-activated cyclic nucleo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0094 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP | |||||||||
Map data | Sharpened cryosparc map used for building and refinement | |||||||||
Sample |
| |||||||||
Keywords | ION CHANNEL / PACEMAKER CURRENT / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / HCN channel complex / membrane depolarization during SA node cell action potential / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity ...voltage-gated potassium channel activity involved in SA node cell action potential depolarization / sinoatrial node development / HCN channels / regulation of cardiac muscle cell action potential involved in regulation of contraction / SA node cell action potential / HCN channel complex / membrane depolarization during SA node cell action potential / cellular response to cGMP / regulation of membrane depolarization / intracellularly cAMP-activated cation channel activity / membrane depolarization during cardiac muscle cell action potential / sodium ion import across plasma membrane / blood circulation / voltage-gated sodium channel activity / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium ion import across plasma membrane / monoatomic cation transport / regulation of cardiac muscle contraction / sodium ion transmembrane transport / cAMP binding / cellular response to cAMP / potassium ion transmembrane transport / muscle contraction / regulation of heart rate / regulation of membrane potential / axon / dendrite / perinuclear region of cytoplasm / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Shintre CA / Pike ACW | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel Authors: Shintre CA / Pike ACW / Tessitore A / Young M / Bushell SR / Strain-Damerell C / Mukhopadhyay S / Burgess-Brown NA / Huiskonen JT / Arrowsmith CH / Edwards AM / Bountra C / Carpenter EP | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0094.map.gz | 38.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0094-v30.xml emd-0094.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0094_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_0094.png | 181.4 KB | ||
Masks | emd_0094_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-0094.cif.gz | 6.8 KB | ||
Others | emd_0094_additional.map.gz emd_0094_half_map_1.map.gz emd_0094_half_map_2.map.gz | 20.3 MB 37.2 MB 37.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0094 | HTTPS FTP |
-Validation report
Summary document | emd_0094_validation.pdf.gz | 190.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0094_full_validation.pdf.gz | 189.9 KB | Display | |
Data in XML | emd_0094_validation.xml.gz | 501 B | Display | |
Data in CIF | emd_0094_validation.cif.gz | 370 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0094 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0094 | HTTPS FTP |
-Related structure data
Related structure data | 6gyoMC 0093C 6gynC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0094.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened cryosparc map used for building and refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_0094_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Original cryosparc map
File | emd_0094_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Original cryosparc map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map1
File | emd_0094_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map2
File | emd_0094_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...
Entire | Name: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4 |
---|---|
Components |
|
-Supramolecule #1: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-ga...
Supramolecule | Name: Potassium/Sodium hyperpolarization-activated cyclic nucleotide-gated ion channel 4 type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.836754 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE ...String: SMLPEAEVRL GQAGFMQRQF GAMLQPGVNK FSLRMFGSQK AVEREQERVK SAGFWIIHPY SDFRFYWDLT MLLLMVGNLI IIPVGITFF KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI SSIPVDYIFL I VETRIDSE VYKTARALRI VRFTKILSLL RLLRLSRLIR YIHQWEEIFH MTYDLASAVV RIVNLIGMML LLCHWDGCLQ FL VPMLQDF PDDCWVSINN MVNNSWGKQY SYALFKAMSH MLCIGYGRQA PVGMSDVWLT MLSMIVGATC YAMFIGHATA LIQ SLDSSR RQYQEKYKQV EQYMSFHKLP PDTRQRIHDY YEHRYQGKMF DEESILGELS EPLREEIINF NCRKLVASMP LFAN ADPNF VTSMLTKLRF EVFQPGDYII REGTIGKKMY FIQHGVVSVL TKGNKETKLA DGSYFGEICL LTRGRRTASV RADTY CRLY SLSVDNFNEV LEEYPMMRRA FETVALDRLD RIGKKNS UniProtKB: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 |
-Macromolecule #2: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Macromolecule | Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CMP |
---|---|
Molecular weight | Theoretical: 329.206 Da |
Chemical component information | ChemComp-CMP: |
-Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 28 / Formula: PC1 |
---|---|
Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ChemComp-PC1: |
-Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / type: ligand / ID: 4 / Number of copies: 4 / Formula: PIE |
---|---|
Molecular weight | Theoretical: 836.061 Da |
Chemical component information | ChemComp-PIE: |
-Macromolecule #5: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 5 / Number of copies: 8 / Formula: 3PE |
---|---|
Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ChemComp-3PE: |
-Macromolecule #6: UNKNOWN ATOM OR ION
Macromolecule | Name: UNKNOWN ATOM OR ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: UNX |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: blotted for 5.5s before plunge. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Details | EBIC TITAN KRIOS M07 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 2338 / Average exposure time: 16.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 37313 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Initial model was from ligand-free HCN4. Model refined against the cryosparc b-factor sharpened map using default restraints |
---|---|
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-6gyo: |