9DXI | pdb_00009dxi

Crystal structure of dimer Caenorhabditis elegans lipid binding protein 3 (LBP-3)

• PDB DOI: https://doi.org/10.2210/pdb9DXI/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2025-01-22 
• Deposition Author(s): Cuevas, A.R., Tillman, M.C., Ortlund, E.A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.

Cuevas, A.R., Tillman, M.C., Wang, M.C., Ortlund, E.A.

(2025) Protein Sci 34: e5249-e5249

• PubMed: 39660930 
• DOI: https://doi.org/10.1002/pro.5249
• Primary Citation Related Structures: 
  9DXI


• PubMed Abstract: 
  

  Intracellular lipid binding proteins (iLBPs) play crucial roles in lipid transport and cellular metabolism across the animal kingdom. Recently, a fat-to-neuron axis was described in Caenorhabditis elegans, in which lysosomal activity in the fat liberates polyunsaturated fatty acids (PUFAs) that signal to neurons and extend lifespan with durable fecundity. In this study, we investigate the structure and binding mechanisms of a lifespan-extending lipid chaperone, lipid binding protein-3 (LBP-3), which shuttles dihomo-γ-linolenic (DGLA) acid from intestinal fat to neurons. We present the first high-resolution crystal structure of LBP-3, which reveals a classic iLBP fold with an unexpected and unique homodimeric arrangement via interstrand interactions that is incompatible with ligand binding. We identify key ionic interactions that mediate DGLA binding within the lipid binding pocket. Molecular dynamics simulations further elucidate LBP-3's preferential binding to DGLA due to its rotational freedom and access to favorable binding conformations compared to other 20-carbon PUFAs. We also propose that LBP-3 dimerization may be a unique regulatory mechanism for lipid chaperones.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 34.96 kDa 
• Atom Count: 2,360 
• Modeled Residue Count: 279 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein homolog 3	A, B	151	Caenorhabditis elegans	Mutation(s): 0  Gene Names: lbp-3, F40F4.4
UniProt
Find proteins for Q20222 (Caenorhabditis elegans) Explore Q20222  Go to UniProtKB:  Q20222

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.731	α = 90
b = 68.846	β = 90
c = 103.891	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Cuevas, A.R., Tillman, M.C., Ortlund, E.A.

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Funding Organization	Location	Grant Number
Other government	United States	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release