7U9D

Crystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with PC(16:0/20:4)

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

  • Deposited: 2022-03-10 Released: 2023-04-12 
  • Deposition Author(s): Druzak, S.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Ligand dependent interaction between PC-TP and PPAR delta mitigates diet-induced hepatic steatosis in male mice.

Druzak, S.A.Tardelli, M.Mays, S.G.El Bejjani, M.Mo, X.Maner-Smith, K.M.Bowen, T.Cato, M.L.Tillman, M.C.Sugiyama, A.Xie, Y.Fu, H.Cohen, D.E.Ortlund, E.A.

(2023) Nat Commun 14: 2748-2748

  • DOI: https://doi.org/10.1038/s41467-023-38010-w
  • Primary Citation of Related Structures:  
    7U9D

  • PubMed Abstract: 

    Phosphatidylcholine transfer protein (PC-TP; synonym StarD2) is a soluble lipid-binding protein that transports phosphatidylcholine (PC) between cellular membranes. To better understand the protective metabolic effects associated with hepatic PC-TP, we generated a hepatocyte-specific PC-TP knockdown (L-Pctp -/- ) in male mice, which gains less weight and accumulates less liver fat compared to wild-type mice when challenged with a high-fat diet. Hepatic deletion of PC-TP also reduced adipose tissue mass and decreases levels of triglycerides and phospholipids in skeletal muscle, liver and plasma. Gene expression analysis suggest that the observed metabolic changes are related to transcriptional activity of peroxisome proliferative activating receptor (PPAR) family members. An in-cell protein complementation screen between lipid transfer proteins and PPARs uncovered a direct interaction between PC-TP and PPARδ that was not observed for other PPARs. We confirmed the PC-TP- PPARδ interaction in Huh7 hepatocytes, where it was found to repress PPARδ-mediated transactivation. Mutations of PC-TP residues implicated in PC binding and transfer reduce the PC-TP-PPARδ interaction and relieve PC-TP-mediated PPARδ repression. Reduction of exogenously supplied methionine and choline reduces the interaction while serum starvation enhances the interaction in cultured hepatocytes. Together our data points to a ligand sensitive PC-TP- PPARδ interaction that suppresses PPAR activity.


  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylcholine transfer protein214Homo sapiensMutation(s): 0 
Gene Names: PCTPSTARD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL6 (Homo sapiens)
Explore Q9UKL6 
Go to UniProtKB:  Q9UKL6
PHAROS:  Q9UKL6
GTEx:  ENSG00000141179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKL6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M2R (Subject of Investigation/LOI)
Query on M2R

Download Ideal Coordinates CCD File 
B [auth A][(2~{R})-1-hexadecanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate
C44 H81 N O8 P
IIZPXYDJLKNOIY-JXPKJXOSSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.172α = 90
b = 133.172β = 90
c = 83.271γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-04-12 
  • Deposition Author(s): Druzak, S.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesF31DK126435
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK048873

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-04-24
    Changes: Database references