8YEL

Cryo-EM structure of the channelrhodopsin GtCCR4

• PDB DOI: https://doi.org/10.2210/pdb8YEL/pdb
• EM Map EMD-39199: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Guillardia theta
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-02-22 Released: 2024-09-04 
• Deposition Author(s): Tanaka, T., Iida, W., Sano, F.K., Oda, K., Shihoya, W., Nureki, O.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4

Tanaka, T., Hososhima, H., Yamashita, Y., Sugimoto, T., Nakamura, T., Shigemura, S., Iida, W., Sano, F.K., Oda, K., Uchihashi, T., Katayama, K., Furutani, Y., Tsunoda, S.P., Shihoya, W., Kandori, H., Nureki, O.

(2024) Mol Cell 

• DOI: https://doi.org/10.1016/j.molcel.2024.08.016

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 48.59 kDa 
• Atom Count: 2,277 
• Modelled Residue Count: 265 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation channel rhodopsin 4	A	398	Guillardia theta	Mutation(s): 0  Gene Names: CCR4 Membrane Entity: Yes
UniProt
Find proteins for A0A3G1I4H9 (Guillardia theta) Explore A0A3G1I4H9  Go to UniProtKB:  A0A3G1I4H9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC1	C [auth A], D [auth A], E [auth A]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N
RET (Subject of Investigation/LOI)	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Tanaka, T., Iida, W., Sano, F.K., Oda, K., Shihoya, W., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22KJ0577
Japan Society for the Promotion of Science (JSPS)	Japan	19H05777
Japan Society for the Promotion of Science (JSPS)	Japan	22K19371
Japan Society for the Promotion of Science (JSPS)	Japan	22H02751
Japan Society for the Promotion of Science (JSPS)	Japan	21H05037
Japan Agency for Medical Research and Development (AMED)	Japan	JP233fa627001
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121002
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121012

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release