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- EMDB-32377: 2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin... -

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Basic information

Entry
Database: EMDB / ID: EMD-32377
Title2.02 angstrom cryo-EM structure of the pump-like channelrhodopsin ChRmine
Map data
Sample
  • Complex: ChRmine
    • Protein or peptide: ChRmine
  • Ligand: RETINAL
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
  • Ligand: water
Biological speciesRhodomonas lens (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.02 Å
AuthorsKishi KE / Kim Y / Fukuda M / Yamashita K / Deisseroth K / Kato HE
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21wm0525018 Japan
Japan Society for the Promotion of Science (JSPS)21H05142 Japan
Japan Science and TechnologyJPMJPR1782 Japan
Japan Science and TechnologyJPMJFR204S Japan
Japan Science and TechnologyJPMJCR21P3 Japan
Other private Japan
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH075957 Japan
Other private Japan
CitationJournal: Cell / Year: 2022
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
DepositionDec 11, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateMar 9, 2022-
Current statusMar 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7w9w
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7w9w
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32377.png

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Map

FileDownload / File: emd_32377.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 162 pix.
= 152.795 Å		0.94 Å/pix.
x 162 pix.
= 152.795 Å		0.94 Å/pix.
x 162 pix.
= 152.795 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.10222625 - 0.23236215
Average (Standard dev.)0.0006151247 (±0.007928331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions162162162
Spacing162162162
CellA=B=C: 152.79549 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.943179012345680.943179012345680.94317901234568
M x/y/z162162162
origin x/y/z0.0000.0000.000
length x/y/z152.795152.795152.795
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS162162162
D min/max/mean-0.1020.2320.001

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Supplemental data

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Mask #1

Fileemd_32377_msk_1.map
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Half map: #1

Fileemd_32377_half_map_1.map
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Histogram

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Half map: #2

Fileemd_32377_half_map_2.map
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Sample components

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Entire : ChRmine

EntireName: ChRmine
Components
  • Complex: ChRmine
    • Protein or peptide: ChRmine
  • Ligand: RETINAL
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: ChRmine

SupramoleculeName: ChRmine / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhodomonas lens (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: ChRmine

MacromoleculeName: ChRmine / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodomonas lens (eukaryote)
Molecular weightTheoretical: 35.772965 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMAHAPGTD QMFYVGTMDG WYLDTKLNSV AIGAHWSCFI VLTITTFYLG YESWTSRGPS KRTSFYAGYQ EEQNLALFVN FFAMLSYFG KIVADTLGHN FGDVGPFIIG FGNYRYADYM LTCPMLVYDL LYQLRAPYRV SCSAIIFAIL MSGVLAEFYA E GDPRLRNG ...String:
GPMAHAPGTD QMFYVGTMDG WYLDTKLNSV AIGAHWSCFI VLTITTFYLG YESWTSRGPS KRTSFYAGYQ EEQNLALFVN FFAMLSYFG KIVADTLGHN FGDVGPFIIG FGNYRYADYM LTCPMLVYDL LYQLRAPYRV SCSAIIFAIL MSGVLAEFYA E GDPRLRNG AYAWYGFGCF WFIFAYSIVM SIVAKQYSRL AQLAQDTGAE HSLHVLKFAV FTFSMLWILF PLVWAICPRG FG WIDDNWT EVAHCVCDIV AKSCYGFALA RFRKTYDEEL FRLLEQLGHD EDEFQKLELD MRLSSNGERL EVLFQ

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 1 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 5 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 48 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.533 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185895
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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