9MRH | pdb_00009mrh

Fluorescence lifetime-readout citrate sensor

• PDB DOI: https://doi.org/10.2210/pdb9MRH/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-07 Released: 2025-11-12 
• Deposition Author(s): Rosen, P.C., Yellen, G., Lim, D.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Models: experimental

Literature

Activity-dependent citrate dynamics in neurons.

Rosen, P.C., Fu, P., Ferran, B., Kim, E., Brooks, D.J., Lim, D.C., Diaz-Garcia, C.M., Yellen, G.

(2025) Proc Natl Acad Sci U S A 122: e2519902122-e2519902122

• PubMed: 41071660 
• DOI: https://doi.org/10.1073/pnas.2519902122
• Primary Citation of Related Structures:  
  9MRH


• PubMed Abstract: 
  

  Glycolytic enzymes sense metabolite levels to adapt rapidly to changing energy demands, but measuring the levels of these effectors with spatiotemporal precision in live cells has been challenging. We addressed this question in the context of neuronal depolarization, which activates glycolysis, focusing on the glycolysis inhibitor citrate. We engineered a pair of quantitative fluorescent biosensors for citrate that address several limitations (affinity, pH, Mg ²⁺ , and temperature) of existing citrate biosensors. Using two-photon fluorescence lifetime imaging, we found that free citrate in the cytosol of neurons in acute mouse brain slices declines two-to-threefold within seconds of neuronal activation and then returns to baseline over a few minutes. The stimulation-dependent citrate transient depends at least in part on the mitochondrial calcium uniporter. These types of live metabolite measurements are essential for achieving a nuanced understanding of the fast control of glycolysis.

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Organizational Affiliation: 
• Department of Neurobiology, Harvard Medical School, Boston, MA 02115.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
Department of Biochemistry and Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104.
Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104.
Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 86.9 kDa 
• Atom Count: 6,256 
• Modeled Residue Count: 743 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescence lifetime-readout citrate sensor	A, B	383	Aequorea	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	D [auth A], F [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CIT (Subject of Investigation/LOI)	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SWG	A, B	L-PEPTIDE LINKING	C16 H16 N4 O4		SER, TRP, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.44	α = 90
b = 96.19	β = 90
c = 144.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Rosen, P.C., Yellen, G., Lim, D.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM124038

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release