8PQO

PITP in complex with the inhibitor VT01545


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Non-vesicular phosphatidylinositol transfer plays critical roles in defining organelle lipid composition.

Kim, Y.J.Pemberton, J.G.Eisenreichova, A.Mandal, A.Koukalova, A.Rohilla, P.Sohn, M.Konradi, A.W.Tang, T.T.Boura, E.Balla, T.

(2024) EMBO J 43: 2035-2061

  • DOI: https://doi.org/10.1038/s44318-024-00096-3
  • Primary Citation of Related Structures:  
    8PQO

  • PubMed Abstract: 

    Phosphatidylinositol (PI) is the precursor lipid for the minor phosphoinositides (PPIns), which are critical for multiple functions in all eukaryotic cells. It is poorly understood how phosphatidylinositol, which is synthesized in the ER, reaches those membranes where PPIns are formed. Here, we used VT01454, a recently identified inhibitor of class I PI transfer proteins (PITPs), to unravel their roles in lipid metabolism, and solved the structure of inhibitor-bound PITPNA to gain insight into the mode of inhibition. We found that class I PITPs not only distribute PI for PPIns production in various organelles such as the plasma membrane (PM) and late endosomes/lysosomes, but that their inhibition also significantly reduced the levels of phosphatidylserine, di- and triacylglycerols, and other lipids, and caused prominent increases in phosphatidic acid. While VT01454 did not inhibit Golgi PI4P formation nor reduce resting PM PI(4,5)P 2 levels, the recovery of the PM pool of PI(4,5)P 2 after receptor-mediated hydrolysis required both class I and class II PITPs. Overall, these studies show that class I PITPs differentially regulate phosphoinositide pools and affect the overall cellular lipid landscape.


  • Organizational Affiliation

    Section on Molecular Signal Transduction, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol transfer protein alpha isoformA [auth C]270Homo sapiensMutation(s): 0 
Gene Names: PITPNAPITPN
UniProt & NIH Common Fund Data Resources
Find proteins for Q00169 (Homo sapiens)
Explore Q00169 
Go to UniProtKB:  Q00169
PHAROS:  Q00169
GTEx:  ENSG00000174238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00169
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FH6 (Subject of Investigation/LOI)
Query on FH6

Download Ideal Coordinates CCD File 
L [auth C](2~{R})-2-azanyl-3-[(2~{S},3~{R})-2-methyl-5-oxidanylidene-pyrrolidin-3-yl]sulfanyl-propanal
C8 H14 N2 O2 S
DSBMZROJCWDNEG-RRKCRQDMSA-N
F8O (Subject of Investigation/LOI)
Query on F8O

Download Ideal Coordinates CCD File 
G [auth C](2~{R},4~{R})-2,4-dimethyloctanal
C10 H20 O
QOALBYYPDVNTFJ-NXEZZACHSA-N
FDO (Subject of Investigation/LOI)
Query on FDO

Download Ideal Coordinates CCD File 
H [auth C](2~{R})-4-methyl-2-(methylamino)pentanamide
C7 H16 N2 O
FBFNXGHTGRJJHX-ZCFIWIBFSA-N
MV9 (Subject of Investigation/LOI)
Query on MV9

Download Ideal Coordinates CCD File 
J [auth C](2~{R})-3-methyl-2-(methylamino)butanoic acid
C6 H13 N O2
AKCRVYNORCOYQT-RXMQYKEDSA-N
UYA (Subject of Investigation/LOI)
Query on UYA

Download Ideal Coordinates CCD File 
K [auth C](4R)-4-hydroxy-D-proline
C5 H9 N O3
PMMYEEVYMWASQN-QWWZWVQMSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C,
D [auth C],
F [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BU4 (Subject of Investigation/LOI)
Query on BU4

Download Ideal Coordinates CCD File 
I [auth C](3R)-butane-1,3-diol
C4 H10 O2
PUPZLCDOIYMWBV-SCSAIBSYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth C]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth C]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.33α = 90
b = 81.906β = 90
c = 94.701γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references