7ZGC | pdb_00007zgc

Structure of yeast Sec14p with NPPM481

• PDB DOI: https://doi.org/10.2210/pdb7ZGC/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2022-04-03 Released: 2023-01-25 
• Deposition Author(s): Hong, Z., Johnen, P., Schaaf, G., Bono, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.211 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity.

Chen, X.R., Poudel, L., Hong, Z., Johnen, P., Katti, S., Tripathi, A., Nile, A.H., Green, S.M., Khan, D., Schaaf, G., Bono, F., Bankaitis, V.A., Igumenova, T.I.

(2023) J Biological Chem 299: 102861-102861

• PubMed: 36603766 
• DOI: https://doi.org/10.1016/j.jbc.2022.102861
• Primary Citation Related Structures: 
  7ZG9, 7ZGA, 7ZGB, 7ZGC, 7ZGD


• PubMed Abstract: 
  

  Phosphatidylinositol (PtdIns) transfer proteins (PITPs) enhance the activities of PtdIns 4-OH kinases that generate signaling pools of PtdIns-4-phosphate. In that capacity, PITPs serve as key regulators of lipid signaling in eukaryotic cells. Although the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activities, the underlying mechanism is not understood. Herein, we apply an integrative structural biology approach to investigate interactions of the yeast PITP Sec14 with small-molecule inhibitors (SMIs) of its phospholipid exchange cycle. Using a combination of X-ray crystallography, solution NMR spectroscopy, and atomistic MD simulations, we dissect how SMIs compete with native Sec14 phospholipid ligands and arrest phospholipid exchange. Moreover, as Sec14 PITPs represent new targets for the development of next-generation antifungal drugs, the structures of Sec14 bound to SMIs of diverse chemotypes reported in this study will provide critical information required for future structure-based design of next-generation lead compounds directed against Sec14 PITPs of virulent fungi.

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Organizational Affiliation: 
• Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA.
Max Planck Institute for Developmental Biology, Tübingen, Germany.
Institute for Crop Science and Resource Conservation, Universität Bonn, Bonn, Germany.
Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA.
Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA.
Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA; Department of Cell Biology & Genetics, Texas A&M University, College Station, Texas, USA. Electronic address: [e-mail].
Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.51 kDa 
• Atom Count: 2,389 
• Modeled Residue Count: 298 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEC14 cytosolic factor	A	312	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SEC14, PIT1, YMR079W, YM9582.04 Membrane Entity: Yes
UniProt
Find proteins for P24280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24280  Go to UniProtKB:  P24280

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUO (Subject of Investigation/LOI)	B [auth A]	(4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone C17 H15 Cl F N3 O3 LSPJXCGEFJDMHA-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.211 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.217	α = 90
b = 86.217	β = 90
c = 109.657	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Hong, Z., Johnen, P., Schaaf, G., Bono, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description