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- EMDB-40063: Cation channelrhodopsin from Hyphochytrium catenoides (HcCCR) emb... -
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Open data
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Basic information
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Title | Cation channelrhodopsin from Hyphochytrium catenoides (HcCCR) embedded in peptidisc | ||||||||||||
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![]() | Retinal Protein / Channelrhodopsin / Cation channel / Peptidisc / Optogenetics / TRANSPORT PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||
![]() | Morizumi T / Kim K / Li H / Spudich JL / Ernst OP | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K and Na selectivities. Authors: Takefumi Morizumi / Kyumhyuk Kim / Hai Li / Elena G Govorunova / Oleg A Sineshchekov / Yumei Wang / Lei Zheng / Éva Bertalan / Ana-Nicoleta Bondar / Azam Askari / Leonid S Brown / John L ...Authors: Takefumi Morizumi / Kyumhyuk Kim / Hai Li / Elena G Govorunova / Oleg A Sineshchekov / Yumei Wang / Lei Zheng / Éva Bertalan / Ana-Nicoleta Bondar / Azam Askari / Leonid S Brown / John L Spudich / Oliver P Ernst / ![]() ![]() ![]() ![]() Abstract: Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K over Na in the absence of the canonical ...Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K over Na in the absence of the canonical tetrameric K selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na channel with >100-fold larger Na to K permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K versus Na selectivity is determined at two distinct sites on the putative ion conduction pathway: in a patch of critical residues in the intracellular segment (Leu69/Phe69, Ile73/Ser73 and Asp116) and within a cluster of aromatic residues in the extracellular segment (primarily, Trp102 and Tyr222). The two filters are on the opposite sides of the photoactive site involved in channel gating. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21 KB 21 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 54.6 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 48.9 MB 48.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 762.3 KB | Display | ![]() |
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Full document | ![]() | 761.9 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40063_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40063_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cation channelrhodopsin trimer reconstituted in peptidisc
Entire | Name: Cation channelrhodopsin trimer reconstituted in peptidisc |
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Components |
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-Supramolecule #1: Cation channelrhodopsin trimer reconstituted in peptidisc
Supramolecule | Name: Cation channelrhodopsin trimer reconstituted in peptidisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.197 KDa |
-Macromolecule #1: Cation Channelrhodopsin
Macromolecule | Name: Cation Channelrhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.224213 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPFCGGRPED GWHHGSIHDM DYPLLGAMAA ICSVFIGGSG AWMLYRLDLG LGYSCKPHHS GYAPEANSFS ALSCLVSGTI YAAKTFDFF DGGGTPFSFN WYWYLDYVFT CPLILLDVLY TLEIPHKLRF VFAVIITLWC GVAAFVTPSA FRFGYYAVGC V WFVPFSFS ...String: MPFCGGRPED GWHHGSIHDM DYPLLGAMAA ICSVFIGGSG AWMLYRLDLG LGYSCKPHHS GYAPEANSFS ALSCLVSGTI YAAKTFDFF DGGGTPFSFN WYWYLDYVFT CPLILLDVLY TLEIPHKLRF VFAVIITLWC GVAAFVTPSA FRFGYYAVGC V WFVPFSFS LLRHVKQRYQ VYPPKCQKLL FWACTIFFGF WPLFPILFLF SWLGTGHIDQ QAFTIIHAFL DLFCKTVFGL IM TFFRLEL EEHTEVLGLP LNEPKGKH |
-Macromolecule #2: RETINAL
Macromolecule | Name: RETINAL / type: ligand / ID: 2 / Number of copies: 1 / Formula: RET |
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Molecular weight | Theoretical: 284.436 Da |
Chemical component information | ![]() ChemComp-RET: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 3 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 7 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Macromolecule #5: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Macromolecule | Name: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 5 / Number of copies: 2 / Formula: PEE |
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Molecular weight | Theoretical: 744.034 Da |
Chemical component information | ![]() ChemComp-PEE: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 15 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.35 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | Sample was kept in the dark prior to freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5902 / Average electron dose: 40.0 e/Å2 / Details: Falcon 4i detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Initial fitting done in Phenix |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 151.1 / Target criteria: Cross correlation coefficent |
Output model | ![]() PDB-8gi9: |