9N0X | pdb_00009n0x

Cryo-EM structure of human PSS2

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  MemProtMD

  • Deposited: 2025-01-24 Released: 2025-05-07 
  • Deposition Author(s): Li, D.Y., Li, X.C.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular insights into human phosphatidylserine synthase 2 and its regulation of SREBP pathways.

Li, D.Chen, H.Vale, G.Elghobashi-Meinhardt, N.Hatton, A.Rong, S.McDonald, J.G.Li, X.

(2025) Proc Natl Acad Sci U S A 122: e2501177122-e2501177122

  • DOI: https://doi.org/10.1073/pnas.2501177122
  • Primary Citation of Related Structures:  
    9N0X

  • PubMed Abstract: 

    Homologous proteins share similar sequences, enabling them to work together in cells to support normal physiological functions. Phosphatidylserine synthases 1 and 2 (PSS1 and PSS2) are homologous enzymes that catalyze the synthesis of phosphatidylserine (PS) from different substrates. PSS2 shows a preference for phosphatidylethanolamine (PE) as its substrate, whereas PSS1 can utilize either PE or phosphatidylcholine. Previous studies showed that inhibiting PSS1 promotes SREBP-2 cleavage. Interestingly, despite their homology, our findings reveal that PSS2 exerts an opposing effect on the cleavage of both SREBP-1 and SREBP-2. We resolved the cryo-electron microscopy (cryo-EM) structure of human PSS2 at 3.3 Å resolution. Structural comparison of the catalytic cavities between PSS1 and PSS2 along with molecular dynamics simulations uncovers the molecular details behind the substrate preference of PSS2 for PE. The lipidomic analysis showed that PSS2 deficiency leads to PE accumulation in the endoplasmic reticulum, which has been shown to inhibit the cleavage of sterol regulatory element-binding proteins (SREBPs) in mice. Thus, our findings reveal the intricate network of intracellular phospholipid metabolism and underscore the distinct regulatory roles of homologous proteins in cellular activities.


  • Organizational Affiliation
    • Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylserine synthase 2
A, B
487Homo sapiensMutation(s): 0 
Gene Names: PTDSS2PSS2
EC: 2.7.8.29
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVG9 (Homo sapiens)
Explore Q9BVG9 
Go to UniProtKB:  Q9BVG9
PHAROS:  Q9BVG9
GTEx:  ENSG00000174915 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVG9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P5S (Subject of Investigation/LOI)
Query on P5S

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
RXY (Subject of Investigation/LOI)
Query on RXY

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
(7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphapentacos-7-en-19-yl (9Z)-octadec-9-enoate
C39 H74 N O8 P
RAMNOXDFBNFSFC-AVWHJSSGSA-N
CA (Subject of Investigation/LOI)
Query on CA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection
  • Version 1.2: 2025-11-19
    Changes: Data collection, Database references