+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25135 | |||||||||
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Title | Apo-ChRmine in MSP1E3D1 lipid nanodisc | |||||||||
Map data | Apo-ChRmine in MSP1E3D1 lipid nanodisc | |||||||||
Sample |
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Keywords | Channelrhodopsin / ion channel / MEMBRANE PROTEIN | |||||||||
Biological species | Tiarina fusa (eukaryote) / Rhodomonas lens (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Tucker K / Brohawn S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs. Authors: Kyle Tucker / Savitha Sridharan / Hillel Adesnik / Stephen G Brohawn / Abstract: Microbial channelrhodopsins are light-gated ion channels widely used for optogenetic manipulation of neuronal activity. ChRmine is a bacteriorhodopsin-like cation channelrhodopsin (BCCR) more closely ...Microbial channelrhodopsins are light-gated ion channels widely used for optogenetic manipulation of neuronal activity. ChRmine is a bacteriorhodopsin-like cation channelrhodopsin (BCCR) more closely related to ion pump rhodopsins than other channelrhodopsins. ChRmine displays unique properties favorable for optogenetics including high light sensitivity, a broad, red-shifted activation spectrum, cation selectivity, and large photocurrents, while its slow closing kinetics impedes some applications. The structural basis for ChRmine function, or that of any other BCCR, is unknown. Here, we present cryo-EM structures of ChRmine in lipid nanodiscs in apo (opsin) and retinal-bound (rhodopsin) forms. The structures reveal an unprecedented trimeric architecture with a lipid filled central pore. Large electronegative cavities on either side of the membrane facilitate high conductance and selectivity for cations over protons. The retinal binding pocket structure suggests channel properties could be tuned with mutations and we identify ChRmine variants with ten-fold decreased and two-fold increased closing rates. A T119A mutant shows favorable properties relative to wild-type and previously reported ChRmine variants for optogenetics. These results provide insight into structural features that generate an ultra-potent microbial opsin and provide a platform for rational engineering of channelrhodopsins with improved properties that could expand the scale, depth, and precision of optogenetic experiments. | |||||||||
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_25135.map.gz | 38.4 MB | EMDB map data format | |
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Header (meta data) | emd-25135-v30.xml emd-25135.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_25135.png | 117.4 KB | ||
Filedesc metadata | emd-25135.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25135 | HTTPS FTP |
-Validation report
Summary document | emd_25135_validation.pdf.gz | 553.2 KB | Display | EMDB validaton report |
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Full document | emd_25135_full_validation.pdf.gz | 552.7 KB | Display | |
Data in XML | emd_25135_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_25135_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25135 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25135 | HTTPS FTP |
-Related structure data
Related structure data | 7shsMC 7sfjC 7sfkC 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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-Map
File | Download / File: emd_25135.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Apo-ChRmine in MSP1E3D1 lipid nanodisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.137 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ChRmine trimer
Entire | Name: ChRmine trimer |
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Components |
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-Supramolecule #1: ChRmine trimer
Supramolecule | Name: ChRmine trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Tiarina fusa (eukaryote) |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: ChRmine
Macromolecule | Name: ChRmine / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Rhodomonas lens (eukaryote) |
Molecular weight | Theoretical: 36.471758 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: (AYA)HAPGTDQMF YVGTMDGWYL DTKLNSVAIG AHWSCFIVLT ITTFYLGYES WTSRGPSKRT SFYAGYQEEQ NLALFV NFF AMLSYFGKIV ADTLGHNFGD VGPFIIGFGN YRYADYMLTC PMLVYDLLYQ LRAPYRVSCS AIIFAILMSG VLAEFYA EG DPRLRNGAYA ...String: (AYA)HAPGTDQMF YVGTMDGWYL DTKLNSVAIG AHWSCFIVLT ITTFYLGYES WTSRGPSKRT SFYAGYQEEQ NLALFV NFF AMLSYFGKIV ADTLGHNFGD VGPFIIGFGN YRYADYMLTC PMLVYDLLYQ LRAPYRVSCS AIIFAILMSG VLAEFYA EG DPRLRNGAYA WYGFGCFWFI FAYSIVMSIV AKQYSRLAQL AQDTGAEHSL HVLKFAVFTF SMLWILFPLV WAICPRGF G WIDDNWTEVA HCVCDIVAKS CYGFALARFR KTYDEELFRL LEQLGHDEDE FQKLELDMRL SSNGERLRRL SLNSLEVLF Q |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 14.4 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |