9B4G

Structure of inhibitor-bound human PSS1

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-03-20 Released: 2024-09-04 
  • Deposition Author(s): Long, T., Li, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake.

Long, T.Li, D.Vale, G.Jiang, Y.Schmiege, P.Yang, Z.J.McDonald, J.G.Li, X.

(2024) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2024.08.004
  • Primary Citation of Related Structures:  
    9B4E, 9B4F, 9B4G

  • PubMed Abstract: 

    In mammalian cells, two phosphatidylserine (PS) synthases drive PS synthesis. Gain-of-function mutations in the Ptdss1 gene lead to heightened PS production, causing Lenz-Majewski syndrome (LMS). Recently, pharmacological inhibition of PSS1 has been shown to suppress tumorigenesis. Here, we report the cryo-EM structures of wild-type human PSS1 (PSS1 WT ), the LMS-causing Pro269Ser mutant (PSS1 P269S ), and PSS1 WT in complex with its inhibitor DS55980254. PSS1 contains 10 transmembrane helices (TMs), with TMs 4-8 forming a catalytic core in the luminal leaflet. These structures revealed a working mechanism of PSS1 akin to the postulated mechanisms of the membrane-bound O-acyltransferase family. Additionally, we showed that both PS and DS55980254 can allosterically inhibit PSS1 and that inhibition by DS55980254 activates the SREBP pathways, thus enhancing the expression of LDL receptors and increasing cellular LDL uptake. This work uncovers a mechanism of mammalian PS synthesis and suggests that selective PSS1 inhibitors have the potential to lower blood cholesterol levels.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylserine synthase 1
A, B
409Homo sapiensMutation(s): 0 
Gene Names: PTDSS1KIAA0024PSSA
EC: 2.7.8.29
UniProt & NIH Common Fund Data Resources
Find proteins for P48651 (Homo sapiens)
Explore P48651 
Go to UniProtKB:  P48651
PHAROS:  P48651
GTEx:  ENSG00000156471 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48651
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AIS
Query on A1AIS

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
(2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate
C41 H79 O13 P
IBUKXRINTKQBRQ-ZKEAXKCJSA-N
P5S
Query on P5S

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth B],
M [auth B]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
LBN
Query on LBN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth A],
K [auth B],
N [auth B]
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
6OU
Query on 6OU

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N
A1AIT (Subject of Investigation/LOI)
Query on A1AIT

Download Ideal Coordinates CCD File 
I [auth A],
R [auth B]
(7P)-7-[(4S)-4-{4-[3,5-bis(trifluoromethyl)phenoxy]phenyl}-5-(2,2-difluoropropyl)-6-oxo-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazol-3-yl]-1,3-benzoxazol-2(3H)-one
C29 H18 F8 N4 O4
OFKFAYQYNRXLHR-QHCPKHFHSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17_3644:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135343

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Data collection, Database references