+Open data
-Basic information
Entry | Database: PDB / ID: 8zap | ||||||
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Title | ExoC110T class 1 channelrhodopsin | ||||||
Components | C110T-class1 | ||||||
Keywords | MEMBRANE PROTEIN / Channelrhodopsin | ||||||
Function / homology | : / RETINAL Function and homology information | ||||||
Biological species | Hyphochytrium catenoides (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Zhang, M.F. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zap.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zap.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 8zap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zap_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8zap_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8zap_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 8zap_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/8zap ftp://data.pdbj.org/pub/pdb/validation_reports/za/8zap | HTTPS FTP |
-Related structure data
Related structure data | 39883MC 8zamC 8zanC 8zaoC 8zaqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 29854.945 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphochytrium catenoides (eukaryote) / Production host: Homo sapiens (human) #2: Chemical | ChemComp-K / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: exoC110T / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Hyphochytrium catenoides (eukaryote) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154800 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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