6LNP | pdb_00006lnp

Crystal structure of citrate Biosensor

• PDB DOI: https://doi.org/10.2210/pdb6LNP/pdb

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


• Deposited: 2019-12-31 Released: 2020-05-06 
• Deposition Author(s): Wen, Y., Campbell, R.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.282 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

High-Performance Intensiometric Direct- and Inverse-Response Genetically Encoded Biosensors for Citrate.

Zhao, Y., Shen, Y., Wen, Y., Campbell, R.E.

(2020) ACS Cent Sci 6: 1441-1450

• PubMed: 32875085 
• DOI: https://doi.org/10.1021/acscentsci.0c00518
• Primary Citation Related Structures: 
  6LNP


• PubMed Abstract: 
  

  Motivated by the growing recognition of citrate as a central metabolite in a variety of biological processes associated with healthy and diseased cellular states, we have developed a series of high-performance genetically encoded citrate biosensors suitable for imaging of citrate concentrations in mammalian cells. The design of these biosensors was guided by structural studies of the citrate-responsive sensor histidine kinase and took advantage of the same conformational changes proposed to propagate from the binding domain to the catalytic domain. Following extensive engineering based on a combination of structure guided mutagenesis and directed evolution, we produced an inverse-response biosensor (Δ F / F _min ≈ 18) designated Citroff1 and a direct-response biosensor (Δ F / F _min ≈ 9) designated Citron1. We report the X-ray crystal structure of Citron1 and demonstrate the utility of both biosensors for qualitative and quantitative imaging of steady-state and pharmacologically perturbed citrate concentrations in live cells.

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Organizational Affiliation: 
• Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
Department of Talent Highland, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.13 kDa 
• Atom Count: 5,578 
• Modeled Residue Count: 733 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA	A [auth B], B [auth D]	403	Aequorea victoria, Klebsiella pneumoniae	Mutation(s): 0  EC: 2.7.13.3
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for P52687 (Klebsiella pneumoniae) Explore P52687  Go to UniProtKB:  P52687
UniProt Groups	P42212P52687

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT (Subject of Investigation/LOI)	C [auth B], D	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A [auth B], B [auth D]	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.282 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.41	α = 90
b = 92.41	β = 90
c = 123.02	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 

& Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Wen, Y., Campbell, R.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870132

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence