10BZ | pdb_000010bz

Structure of human PTDSS1 in complex with calcium

• PDB DOI: https://doi.org/10.2210/pdb10BZ/pdb
• EM Map EMD-75057: EMDB EMDataResource

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


• Deposited: 2026-01-11 Released: 2026-10-28 
• Deposition Author(s): Lie, W., Ming, Z.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of substrate recognition and catalysis in a mammalian phosphatidylserine synthase 2.

Wang, L., Zhang, Z., Yang, H., Laganowsky, A., Zhou, M.

(2026) Proc Natl Acad Sci U S A 123: e2607382123-e2607382123

• PubMed: 42809401 
• DOI: https://doi.org/10.1073/pnas.2607382123
• Primary Citation Related Structures: 
  10BW, 10BX, 10BY, 10BZ, 37JU


• PubMed Abstract: 
  

  Mammalian phosphatidylserine synthase-1 and -2, PSS1 and PSS2, synthesize phosphatidylserine (PS) by replacing the headgroup of either phosphatidylcholine or phosphatidylethanolamine (PE) with a serine. We determined structures of PSS2 from Equus caballus in complex with either a PE or a serine substrate to resolutions of 2.8 to 3.2 Å. The structures define substrate binding sites and reveal that the phosphate group of the PE is coordinated by two Ca ²⁺ . In addition, we found that PSS2 has significant phospholipase D (PLD) activity in the absence of serine and that Ca ²⁺ is required for the PLD activity. These findings enrich and refine our knowledge in the mechanisms of substrate recognition and catalysis in mammalian PSS.

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Organizational Affiliation: 
• Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030.
Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030.
Department of Chemistry, Texas A&M University, College Station, TX 77843.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 111.34 kDa 
• Atom Count: 5,670 
• Modeled Residue Count: 678 
• Deposited Residue Count: 946 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylserine synthase 1	A, B	473	Homo sapiens	Mutation(s): 0  Gene Names: PTDSS1, KIAA0024, PSSA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Lie, W., Ming, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release