7E9Y

Crystal structure of eLACCO1

• PDB DOI: https://doi.org/10.2210/pdb7E9Y/pdb

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


• Deposited: 2021-03-05 Released: 2021-12-22 
• Deposition Author(s): Wen, Y., Campbell, R.E., Lemieux, M.J., Nasu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Models: experimental

Literature

A genetically encoded fluorescent biosensor for extracellular L-lactate.

Nasu, Y., Murphy-Royal, C., Wen, Y., Haidey, J.N., Molina, R.S., Aggarwal, A., Zhang, S., Kamijo, Y., Paquet, M.E., Podgorski, K., Drobizhev, M., Bains, J.S., Lemieux, M.J., Gordon, G.R., Campbell, R.E.

(2021) Nat Commun 12: 7058-7058

• PubMed: 34873165 
• DOI: https://doi.org/10.1038/s41467-021-27332-2
• Primary Citation of Related Structures:  
  7E9Y


• PubMed Abstract: 
  

  L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.

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Organizational Affiliation: 

Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.19 kDa 
• Atom Count: 5,028 
• Modelled Residue Count: 564 
• Deposited Residue Count: 619 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactate-binding periplasmic protein TTHA0766,Lactate-binding periplasmic protein TTHA0766	A	619	Thermus thermophilus HB8, Thermus thermophilus	Mutation(s): 3  Gene Names: TTHA0766
UniProt
Find proteins for Q5SK82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK82  Go to UniProtKB:  Q5SK82

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
CRO	A	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.217	α = 90
b = 104.983	β = 90
c = 138.748	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Wen, Y., Campbell, R.E., Lemieux, M.J., Nasu, Y.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2023-11-29
  Changes: Refinement description