9UPM | pdb_00009upm

Cryo-EM structure of macaque red cone pigment with Q114N mutation

• PDB DOI: https://doi.org/10.2210/pdb9UPM/pdb
• EM Map EMD-64397: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Macaca fascicularis, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-04-28 Released: 2026-06-24 
• Deposition Author(s): Ohashi, S., Kojima, A., Fukuda, M., Kim, S., Kato, H.E., Kandori, H., Katayama, K.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into spectral tuning and retinal exchange in cone visual pigments.

Ohashi, S., Katayama, K., Kojima, A., Yang, X., Fukuda, M., Sacchetta, F., Suno, R., Sugita, Y., Nuemket, N., Kim, S., Kobayashi, K., Imai, H., Iwata, S., Nango, E., Kobayashi, T., Noda, T., Olivucci, M., Kato, H.E., Kandori, H.

(2026) Science 392: eadz3996-eadz3996

• PubMed: 42348681 
• DOI: https://doi.org/10.1126/science.adz3996
• Primary Citation Related Structures: 
  9UPM, 9UPN, 9UPO


• PubMed Abstract: 
  

  Color vision in catarrhine primates relies on red-, green-, and blue-sensitive cone pigments that share an 11- cis -retinal chromophore but differ in absorption maxima. Red and green pigments arose by recent gene duplication and differ at only a few residues. Here, we report cryo-electron microscopy structures of red and green cone pigments from the cynomolgus macaque ( Macaca fascicularis ) integrated with low-temperature vibrational spectroscopy and quantum mechanical and molecular mechanical modeling. The red-green spectral shift is dominated by threonine 285, the hydroxyl dipole of which modulates chromophore electrostatics, whereas steric effects appear modest. We also identified membrane-facing lateral openings in cone pigments but not in inactive rhodopsin. Comparisons with active-state structures suggest activation-dependent gating, and mutational and spectroscopic analyses support a role for this opening in retinal uptake and rapid pigment regeneration.

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Organizational Affiliation: 
• Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.
OptoBioTechnology Research Center, Nagoya, Japan.
FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo, Japan.
Department of Life Sciences, School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, Japan.
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
Kansai Medical University, Hirakata, Japan.
Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Japan Synchrotron Radiation Research Institute, Harima, Japan.
RIKEN Spring-8 Center, Harima, Japan.
Institute for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan.
The Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan.
Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 50.21 kDa 
• Atom Count: 2,338 
• Modeled Residue Count: 294 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LW opsin,Soluble cytochrome b562	A	452	Macaca fascicularis, Escherichia coli	Mutation(s): 4
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9XSX4 (Macaca fascicularis) Explore Q9XSX4  Go to UniProtKB:  Q9XSX4
UniProt Groups	P0ABE7Q9XSX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Ohashi, S., Kojima, A., Fukuda, M., Kim, S., Kato, H.E., Kandori, H., Katayama, K.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJFR204S
Japan Science and Technology	Japan	JPMJPR19G4
Japan Science and Technology	Japan	JPMJCR21P3
Japan Science and Technology	Japan	JPMJCR1753
Japan Science and Technology	Japan	JPMJCR23B1
Japan Science and Technology	Japan	JPMJAX222F
Japan Science and Technology	Japan	JPMJSP2112
Japan Science and Technology	Japan	JPMJPR24OF
Japan Society for the Promotion of Science (JSPS)	Japan	22H00400
Japan Society for the Promotion of Science (JSPS)	Japan	21H04969
Japan Society for the Promotion of Science (JSPS)	Japan	22K19265
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H04742
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K14142
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02262
Japan Society for the Promotion of Science (JSPS)	Japan	25K09525

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Data collection, Database references