9EBX | pdb_00009ebx

Chimeric fluorescence biosensor formed from a lactate-binding protein and GFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

State-dependent motion of a genetically encoded fluorescent biosensor.

Rosen, P.C.Horwitz, S.M.Brooks, D.J.Kim, E.Ambarian, J.A.Waidmann, L.Davis, K.M.Yellen, G.

(2025) Proc Natl Acad Sci U S A 122: e2426324122-e2426324122

  • DOI: https://doi.org/10.1073/pnas.2426324122
  • Primary Citation of Related Structures:  
    9EBW, 9EBX

  • PubMed Abstract: 

    Genetically encoded biosensors can measure biochemical properties such as small-molecule concentrations with single-cell resolution, even in vivo. Despite their utility, these sensors are "black boxes": Very little is known about the structures of their low- and high-fluorescence states or what features are required to transition between them. We used LiLac, a lactate biosensor with a quantitative fluorescence-lifetime readout, as a model system to address these questions. X-ray crystal structures and engineered high-affinity metal bridges demonstrate that LiLac exhibits a large interdomain twist motion that pulls the fluorescent protein away from a "sealed," high-lifetime state in the absence of lactate to a "cracked," low-lifetime state in its presence. Understanding the structures and dynamics of LiLac will help to think about and engineer other fluorescent biosensors.


  • Organizational Affiliation
    • Department of Neurobiology, Harvard Medical School, Boston, MA 02115.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,Methyl-accepting chemotaxis transducer (TlpC)515Aequorea victoriaHelicobacter pylori 26695Mutation(s): 1 
Gene Names: GFPHP_0082
UniProt
Find proteins for O24911 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O24911 
Go to UniProtKB:  O24911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24911
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SWG
Query on SWG
A
L-PEPTIDE LINKINGC16 H16 N4 O4SER, TRP, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.35α = 97.82
b = 57.98β = 91.43
c = 67.319γ = 104.24
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesR01GM124038
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesF31CA254162
National Science Foundation (NSF, United States)United States1937971

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release