9EBW | pdb_00009ebw

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 234.13 kDa 
  • Atom Count: 14,710 
  • Modeled Residue Count: 1,923 
  • Deposited Residue Count: 2,060 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Green fluorescent protein,Methyl-accepting chemotaxis transducer (TlpC)
A, B, C, D
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.285 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.878α = 90
b = 109.803β = 110.14
c = 123.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence