8ZAM | pdb_00008zam

EndoChR2 channelrhodopsin

• PDB DOI: https://doi.org/10.2210/pdb8ZAM/pdb
• EM Map EMD-39880: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-04-25 Released: 2024-09-11 
• Deposition Author(s): Zhang, M.F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Channelrhodopsins with distinct chromophores and binding patterns.

Shan, Y., Zhao, L., Chen, M., Li, X., Zhang, M., Pei, D.

(2024) Nat Commun 15: 7292-7292

• PubMed: 39181878 
• DOI: https://doi.org/10.1038/s41467-024-51811-x
• Primary Citation Related Structures: 
  8ZAM, 8ZAN, 8ZAO, 8ZAP, 8ZAQ


• PubMed 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 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.

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Organizational Affiliation: 
• Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. [e-mail].
Fudan University, Shanghai, China. [e-mail].
Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 71.36 kDa 
• Atom Count: 4,000 
• Modeled Residue Count: 492 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaeal-type opsin 2	A, B	315	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: cop4, acop2, CSOB, CHLRE_02g085257v5 Membrane Entity: Yes
UniProt
Find proteins for Q8RUT8 (Chlamydomonas reinhardtii) Explore Q8RUT8  Go to UniProtKB:  Q8RUT8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L9Q (Subject of Investigation/LOI)	C [auth A], D [auth B]	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C41 H80 N O8 P JQKOHRZNEOQNJE-VYCVAHKRSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Zhang, M.F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary