9KQJ | pdb_00009kqj

Cryo-EM structure of PSS1 with calcium

PDB DOI: https://doi.org/10.2210/pdb9KQJ/pdb
EM Map EMD-62506: EMDB EMDataResource

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

Deposited: 2024-11-26 Released: 2025-04-02
Deposition Author(s): Ning, Y., Yu, J., Ge, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for catalytic mechanism of human phosphatidylserine synthase 1.

Ning, Y., Xu, R., Yu, J., Ge, J.

(2025) Cell Discov 11: 20-20

PubMed: 40044636 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-025-00775-3
Primary Citation of Related Structures:
9KQF, 9KQI, 9KQJ

Organizational Affiliation

School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 123.2 kDa
Atom Count: 7,056
Modeled Residue Count: 754
Deposited Residue Count: 946
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Membrane Entity: Yes
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T7X (Subject of Investigation/LOI) Query on T7X Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B]	L [auth A], N [auth B]	Phosphatidylinositol C₄₇ H₈₃ O₁₃ P KRTOMQDUKGRFDJ-TWUHCGEESA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Interactions & Density Focus chain L [auth A] Focus chain N [auth B]
LBN (Subject of Investigation/LOI) Query on LBN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain R [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain R [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain R [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] I [auth A] J [auth A] M [auth A] E [auth A], F [auth A], I [auth A], J [auth A], M [auth A], O [auth B], R [auth B], S [auth B], V [auth B], W [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B]
PSF (Subject of Investigation/LOI) Query on PSF Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], P [auth B], Q [auth B]	1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE C₁₈ H₃₄ N O₁₀ P MIQYPPGTNIFAPO-CABCVRRESA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain P [auth B] Focus chain Q [auth B]
C14 Query on C14 Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain H [auth A]	H [auth A], U [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain U [auth B]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B]	G [auth A], T [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain K [auth A] MOL2 format, chain X [auth B] MOL2 format, chain K [auth A] mmCIF format, chain X [auth B] mmCIF format, chain K [auth A]	K [auth A], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain X [auth B]