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- EMDB-39880: EndoChR2 channelrhodopsin -

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Basic information

Entry
Database: EMDB / ID: EMD-39880
TitleEndoChR2 channelrhodopsin
Map data
Sample
  • Complex: endoChR2
    • Protein or peptide: Archaeal-type opsin 2
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
KeywordsChannelrhodopsin / MEMBRANE PROTEIN
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / plasma membrane / Archaeal-type opsin 2
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Channelrhodopsins with distinct chromophores and binding patterns.
Authors: Yuanyue Shan / Liping Zhao / Meiyu Chen / Xiao Li / Mingfeng Zhang / Duanqing Pei /
Abstract: Channelrhodopsins are popular optogenetic tools in neuroscience, but remain poorly understood mechanistically. Here we report the cryo-EM structures of channelrhodopsin-2 (ChR2) from Chlamydomonas ...Channelrhodopsins are popular optogenetic tools in neuroscience, but remain poorly understood mechanistically. Here we report the cryo-EM structures of channelrhodopsin-2 (ChR2) from Chlamydomonas reinhardtii and H. catenoides kalium channelrhodopsin (KCR1). We show that ChR2 recruits an endogenous N-retinylidene-PE-like molecule to a previously unidentified lateral retinal binding pocket, exhibiting a reduced light response in HEK293 cells. In contrast, H. catenoides kalium channelrhodopsin (KCR1) binds an endogenous retinal in its canonical retinal binding pocket under identical condition. However, exogenous ATR reduces the photocurrent magnitude of wild type KCR1 and also inhibits its leaky mutant C110T. Our results uncover diverse retinal chromophores with distinct binding patterns for channelrhodopsins in mammalian cells, which may further inspire next generation optogenetics for complex tasks such as cell fate control.
History
DepositionApr 25, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39880.png

Downloads & links

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Map

FileDownload / File: emd_39880.map.gz / Format: CCP4 / Size: 1000 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.)
0.35 Å/pix.
x 640 pix.
= 224. Å		0.35 Å/pix.
x 640 pix.
= 224. Å		0.35 Å/pix.
x 640 pix.
= 224. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.17779247 - 0.29147416
Average (Standard dev.)-0.00007780258 (±0.006819467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39880_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_39880_half_map_2.map
Projections & Slices
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Sample components

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Entire : endoChR2

EntireName: endoChR2
Components
  • Complex: endoChR2
    • Protein or peptide: Archaeal-type opsin 2
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: endoChR2

SupramoleculeName: endoChR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Archaeal-type opsin 2

MacromoleculeName: Archaeal-type opsin 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 34.93148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYGGALSAV GRELLFVTNP VVVNGSVLVP EDQCYCAGWI ESRGTNGAQT ASNVLQWLAA GFSILLLMFY AYQTWKSTCG WEEIYVCAI EMVKVILEFF FEFKNPSMLY LATGHRVQWL RYAEWLLTCP VILIHLSNLT GLSNDYSRRT MGLLVSDIGT I VWGATSAM ...String:
MDYGGALSAV GRELLFVTNP VVVNGSVLVP EDQCYCAGWI ESRGTNGAQT ASNVLQWLAA GFSILLLMFY AYQTWKSTCG WEEIYVCAI EMVKVILEFF FEFKNPSMLY LATGHRVQWL RYAEWLLTCP VILIHLSNLT GLSNDYSRRT MGLLVSDIGT I VWGATSAM ATGYVKVIFF CLGLCYGANT FFHAAKAYIE GYHTVPKGRC RQVVTGMAWL FFVSWGMFPI LFILGPEGFG VL SVYGSTV GHTIIDLMSK NCWGLLGHYL RVLIHEHILI HGDIRKTTKL NIGGTEIEVE TLVEDEAEAG AVNKGTGK

UniProtKB: Archaeal-type opsin 2

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Macromolecule #2: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadeca...

MacromoleculeName: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: L9Q
Molecular weightTheoretical: 746.05 Da
Chemical component information

ChemComp-L9Q:
(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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