9KQI | pdb_00009kqi

Cryo-EM structure of PSS1 with calcium and L-serine

PDB DOI: https://doi.org/10.2210/pdb9KQI/pdb
EM Map EMD-62505: EMDB EMDataResource

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

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: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KQI

This is version 1.1 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-025-00775-3
Primary Citation Related Structures:
9KQF, 9KQI, 9KQJ

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 123.41 kDa
Atom Count: 7,082
Modeled Residue Count: 754
Deposited Residue Count: 946
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 R [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain E [auth A]	E [auth A], R [auth B]	Phosphatidylinositol C₄₇ H₈₃ O₁₃ P KRTOMQDUKGRFDJ-TWUHCGEESA-N		Interactions Focus chain E [auth A] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain R [auth B]
LBN (Subject of Investigation/LOI) Query on LBN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth A] L [auth A] N [auth A] F [auth A], G [auth A], J [auth A], L [auth A], N [auth A], O [auth B], S [auth B], T [auth B], W [auth B], Y [auth B]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B] Focus chain Y [auth B]
PSF (Subject of Investigation/LOI) Query on PSF Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain D [auth A] 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 V [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth B] mmCIF format, chain I [auth A]	I [auth A], V [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain V [auth B]
D12 Query on D12 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]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-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]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain M [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain M [auth A]	M [auth A], Z [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain M [auth A] Focus chain Z [auth B] Interactions & Density Focus chain M [auth A] Focus chain Z [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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		LG-QS-202203-05; 22PJ1410300;32471016

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release
Version 1.1: 2025-10-01
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.