7VCM | pdb_00007vcm

crystal structure of GINKO1

• PDB DOI: https://doi.org/10.2210/pdb7VCM/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-09-03 Released: 2022-07-27 
• Deposition Author(s): Wen, Y., Campbell, R.E., Lemieux, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.203 (DCC) 

Starting Models: experimental

Literature

A sensitive and specific genetically-encoded potassium ion biosensor for in vivo applications across the tree of life.

Wu, S.Y., Wen, Y., Serre, N.B.C., Laursen, C.C.H., Dietz, A.G., Taylor, B.R., Drobizhev, M., Molina, R.S., Aggarwal, A., Rancic, V., Becker, M., Ballanyi, K., Podgorski, K., Hirase, H., Nedergaard, M., Fendrych, M., Lemieux, M.J., Eberl, D.F., Kay, A.R., Campbell, R.E., Shen, Y.

(2022) PLoS Biol 20: e3001772-e3001772

• PubMed: 36067248 
• DOI: https://doi.org/10.1371/journal.pbio.3001772
• Primary Citation Related Structures: 
  7VCM


• PubMed Abstract: 
  

  Potassium ion (K+) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K+ biosensors are promising tools to further improve our understanding of K+-dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K+ biosensor, GINKO1, in the K+-bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K+ biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K+ dynamics in multiple model organisms, including bacteria, plants, and mice.

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Organizational Affiliation: 
• Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
Department of Experimental Plant Biology, Charles University, Prague, Czech Republic.
Center for Translational Neuromedicine, University of Copenhagen, Copenhagen, Denmark.
Department of Physics, University of California at San Diego, La Jolla, California, United States of America.
Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America.
Department of Physiology, University of Alberta, Edmonton, Alberta, Canada.
GM/CA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America.
Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, New York, United States of America.
Department of Biology, University of Iowa, Iowa City, Iowa, United States of America.
Department of Chemistry, The University of Tokyo, Tokyo, 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: 86.11 kDa 
• Atom Count: 6,703 
• Modeled Residue Count: 742 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Potassium binding protein Kbp,Green fluorescent protein	A, B	386	Aequorea victoria, Escherichia coli K-12	Mutation(s): 10  Gene Names: GFP, kbp
UniProt
Find proteins for P0ADE6 (Escherichia coli (strain K12)) Explore P0ADE6  Go to UniProtKB:  P0ADE6
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
UniProt Groups	P42212P0ADE6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	C [auth A], D [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.203 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.827	α = 89.96
b = 49.319	β = 89.97
c = 83.683	γ = 80.95

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: 2022-07-27 
Deposition Author(s): Wen, Y., Campbell, R.E., Lemieux, M.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	China	FS-154310
National Natural Science Foundation of China (NSFC)	China	No. 31870132 and No. 82072237

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence