7VCM

crystal structure of GINKO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1371/journal.pbio.3001772
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,Potassium binding protein Kbp,Green fluorescent protein
A, B
386Aequorea victoriaEscherichia coli K-12Mutation(s): 10 
Gene Names: GFPkbp
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P0ADE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A, B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.827α = 89.96
b = 49.319β = 89.97
c = 83.683γ = 80.95
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)ChinaFS-154310
National Natural Science Foundation of China (NSFC)ChinaNo. 31870132 and No. 82072237

Revision History  (Full details and data files)

  • 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