8ZMZ | pdb_00008zmz

Cryo-EM structure of R-eLACCO2 in the lactate-bound state

• PDB DOI: https://doi.org/10.2210/pdb8ZMZ/pdb
• EM Map EMD-60263: EMDB EMDataResource

• Classification: FLUORESCENT PROTEIN
• Organism(s): Thermus thermophilus HB8, Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-05-24 Released: 2025-10-29 
• Deposition Author(s): Kamijo, Y., Kusakizako, T., Nureki, O., Campbell, R.E., Nasu, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A red fluorescent genetically encoded biosensor for in vivo imaging of extracellular L-lactate dynamics.

Kamijo, Y., Machler, P., Ness, N., Vu, C.Q., Kusakizako, T., Mannuthodikayil, J., Ku, Z., Boisvert, M., Grebenik, E., Miyazaki, I., Hashizume, R., Sato, H., Liu, R., Hori, Y., Tomita, T., Katayama, T., Furube, A., Caraveo, G., Paquet, M.E., Drobizhev, M., Nureki, O., Arai, S., Brancaccio, M., Campbell, R.E., Kleinfeld, D., Nasu, Y.

(2025) Nat Commun 16: 9531-9531

• PubMed: 41162396 
• DOI: https://doi.org/10.1038/s41467-025-64484-x
• Primary Citation of Related Structures:  
  8ZMZ


• PubMed Abstract: 
  

  L-Lactate is increasingly recognized as an intercellular energy currency in mammals, but mysteries remain regarding the spatial and temporal dynamics of its release and uptake between cells via the extracellular environment. Here we introduce R-eLACCO2.1, a red fluorescent extracellular L-lactate biosensor that is superior to previously reported green fluorescent biosensors in in vivo sensitivity to increases in extracellular L-lactate and spectral orthogonality. R-eLACCO2.1 exhibits excellent fluorescence response in cultured cells, mouse brain slices, and live mice. R-eLACCO2.1 also serves as an effective fluorescence lifetime-based biosensor. Using R-eLACCO2.1, we monitor whisker stimulation and locomotion-induced changes in endogenous extracellular L-lactate in the somatosensory cortex of awake mice. To highlight the potential insights gained from in vivo measurements with R-eLACCO2.1, we perform dual-color imaging from the somatosensory cortex of actively locomoting mice. This enables us to simultaneously observe the neural activity, reported by a green fluorescent GCaMP calcium ion biosensor, and extracellular L-lactate. As the high-performance tool in the suite of extracellular L-lactate biosensors, R-eLACCO2.1 is ideally suited to delimit the emerging roles of L-lactate in mammalian metabolism.

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Organizational Affiliation: 
• Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Department of Physics, University of California San Diego, La Jolla, CA, USA.
Department of Brain Science, Imperial College London, London, UK.
UK Dementia Research Institute at Imperial College London, London, UK.
WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan.
CERVO Brain Research Center, Laval University, Québec, QC, Canada.
Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
Institute of Post-LED Photonics, Tokushima University, Tokushima, Japan.
Department of Anesthesiology and Intensive Care, Laval University, Québec, QC, Canada.
Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Québec, QC, Canada.
Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. [e-mail].
Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan. [e-mail].
Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.17 kDa 
• Atom Count: 4,425 
• Modeled Residue Count: 548 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactate-binding periplasmic protein TTHA0766,Red fluorescent protein drFP583	A	620	Thermus thermophilus HB8, Discosoma sp.	Mutation(s): 58  Gene Names: TTHA0766
UniProt
Find proteins for Q5SK82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK82  Go to UniProtKB:  Q5SK82
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8  Go to UniProtKB:  Q9U6Y8
UniProt Groups	Q9U6Y8Q5SK82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2OP (Subject of Investigation/LOI)	C [auth A]	(2S)-2-HYDROXYPROPANOIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-REOHCLBHSA-N
CA (Subject of Investigation/LOI)	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Kamijo, Y., Kusakizako, T., Nureki, O., Campbell, R.E., Nasu, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--
Japan Science and Technology	Japan	--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Data collection, Database references