9U9D | pdb_00009u9d

Bipartite Genetically Encoded Biosensor sG-GECO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane-Membrane Contact Sites.

Yamaguchi, I.Barazzuol, L.Dematteis, G.Zhu, W.Wen, Y.Drobizhev, M.Lim, D.Campbell, R.E.Cali, T.Nasu, Y.

(2025) Anal Chem 97: 19848-19861

  • DOI: https://doi.org/10.1021/acs.analchem.5c03831
  • Primary Citation of Related Structures:  
    9U9D

  • PubMed Abstract: 

    Self-complementing bipartite fluorescent proteins (FPs) are useful tools for the detection of protein-protein proximity and for localizing fluorophores to membrane-membrane contact sites. Here, we report versions of circularly permuted green FP (GFP), red FP (RFP), and mNeonGreen (NG), which are split into a large fragment composed of nine β-strands and a small fragment composed of two β-strands. In each case, the large and small fragments can associate in live cells to form the complete 11-stranded FP β-barrel. We further converted each of these three self-complementing FPs into bipartite calcium ion (Ca 2+ ) biosensors. We demonstrate that appropriately targeted versions of these split FPs, and split FP-based biosensors, can be functionally assembled at membrane-membrane contact sites. We employ the bipartite NG-based Ca 2+ biosensor for visualization of pharmacologically induced Ca 2+ release at mitochondria-endoplasmic reticulum contact sites (MERCs).


  • Organizational Affiliation
    • Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myosin light chain kinase, smooth muscle, deglutamylated form,Green fluorescent protein,Calmodulin-1234synthetic constructGallus gallusAequorea victoriaRattus norvegicus
This entity is chimeric
Mutation(s): 0 
EC: 2.7.11.18
UniProt
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Find proteins for P11799 (Gallus gallus)
Explore P11799 
Go to UniProtKB:  P11799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DP29P11799
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein232Aequorea victoriaMutation(s): 1 
Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.104α = 90
b = 51.104β = 90
c = 201.306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references