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- PDB-7w9w: 2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin... -
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Basic information
Entry | Database: PDB / ID: 7w9w | |||||||||||||||||||||||||||
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Title | 2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin ChRmine | |||||||||||||||||||||||||||
![]() | ChRmine | |||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / channelrhodopsin / ion channel / photoreceptor / cryo-EM | |||||||||||||||||||||||||||
Function / homology | CHOLESTEROL / PALMITIC ACID / RETINAL![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.02 Å | |||||||||||||||||||||||||||
![]() | Kishi, K.E. / Kim, Y. / Fukuda, M. / Yamashita, K. / Deisseroth, K. / Kato, H.E. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Authors: Koichiro E Kishi / Yoon Seok Kim / Masahiro Fukuda / Masatoshi Inoue / Tsukasa Kusakizako / Peter Y Wang / Charu Ramakrishnan / Eamon F X Byrne / Elina Thadhani / Joseph M Paggi / Toshiki E ...Authors: Koichiro E Kishi / Yoon Seok Kim / Masahiro Fukuda / Masatoshi Inoue / Tsukasa Kusakizako / Peter Y Wang / Charu Ramakrishnan / Eamon F X Byrne / Elina Thadhani / Joseph M Paggi / Toshiki E Matsui / Keitaro Yamashita / Takashi Nagata / Masae Konno / Sean Quirin / Maisie Lo / Tyler Benster / Tomoko Uemura / Kehong Liu / Mikihiro Shibata / Norimichi Nomura / So Iwata / Osamu Nureki / Ron O Dror / Keiichi Inoue / Karl Deisseroth / Hideaki E Kato / ![]() ![]() ![]() Abstract: ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created ...ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology. | |||||||||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32377MC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Multiframe micrographs for Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: C3 (3 fold cyclic)) | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 35772.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-RET / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PLM / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: ChRmine / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 51.533 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0274 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: Dec 3, 2021 Description: (un)restrained refinement or idealisation of macromolecular structures | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185895 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2→88.659 Å / Cor.coef. Fo:Fc: 0.853 / WRfactor Rwork: 0.268 / SU B: 2.42 / SU ML: 0.062 / Average fsc overall: 0.8813 / Average fsc work: 0.8813 / ESU R: 0.065 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.331 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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