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- EMDB-48797: Cryo-EM structure of human PSS2 -

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Basic information

Entry
Database: EMDB / ID: EMD-48797
TitleCryo-EM structure of human PSS2
Map data
Sample
  • Complex: Structure of human PSS2
    • Protein or peptide: Phosphatidylserine synthase 2
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CALCIUM ION
  • Ligand: (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
KeywordsPS lipid / MEMBRANE PROTEIN
Function / homology
Function and homology information


CDP-diacylglycerol-serine O-phosphatidyltransferase activity / L-serine-phosphatidylethanolamine phosphatidyltransferase / L-serine-phosphatidylethanolamine phosphatidyltransferase activity / Synthesis of PS / phosphatidylserine biosynthetic process / transferase activity / endoplasmic reticulum membrane / membrane
Similarity search - Function
Phosphatidyl serine synthase / Phosphatidyl serine synthase
Similarity search - Domain/homology
Phosphatidylserine synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi DY / Li XC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular insights into human phosphatidylserine synthase 2 and its regulation of SREBP pathways.
Authors: Dongyu Li / Hongwen Chen / Goncalo Vale / Nadia Elghobashi-Meinhardt / Alexandra Hatton / Shunxing Rong / Jeffrey G McDonald / Xiaochun Li /
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 ...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.
History
DepositionJan 24, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48797.png

Downloads & links

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Map

FileDownload / File: emd_48797.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.68541425 - 1.1045284
Average (Standard dev.)0.003770684 (±0.0211368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 265.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48797_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48797_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of human PSS2

EntireName: Structure of human PSS2
Components
  • Complex: Structure of human PSS2
    • Protein or peptide: Phosphatidylserine synthase 2
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CALCIUM ION
  • Ligand: (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

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Supramolecule #1: Structure of human PSS2

SupramoleculeName: Structure of human PSS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phosphatidylserine synthase 2

MacromoleculeName: Phosphatidylserine synthase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: L-serine-phosphatidylethanolamine phosphatidyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.30866 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRGERRDAG GPRPESPVPA GRASLEEPPD GPSAGQATGP GEGRRSTESE VYDDGTNTFF WRAHTLTVLF ILTCTLGYVT LLEETPQDT AYNTKRGIVA SILVFLCFGV TQAKDGPFSR PHPAYWRFWL CVSVVYELFL IFILFQTVQD GRQFLKYVDP K LGVPLPER ...String:
MRRGERRDAG GPRPESPVPA GRASLEEPPD GPSAGQATGP GEGRRSTESE VYDDGTNTFF WRAHTLTVLF ILTCTLGYVT LLEETPQDT AYNTKRGIVA SILVFLCFGV TQAKDGPFSR PHPAYWRFWL CVSVVYELFL IFILFQTVQD GRQFLKYVDP K LGVPLPER DYGGNCLIYD PDNETDPFHN IWDKLDGFVP AHFLGWYLKT LMIRDWWMCM IISVMFEFLE YSLEHQLPNF SE CWWDHWI MDVLVCNGLG IYCGMKTLEW LSLKTYKWQG LWNIPTYKGK MKRIAFQFTP YSWVRFEWKP ASSLRRWLAV CGI ILVFLL AELNTFYLKF VLWMPPEHYL VLLRLVFFVN VGGVAMREIY DFMDDPKPHK KLGPQAWLVA AITATELLIV VKYD PHTLT LSLPFYISQC WTLGSVLALT WTVWRFFLRD ITLRYKETRW QKWQNKDDQG STVGNGDQHP LGLDEDLLGP GVAEG EGAP TPN

UniProtKB: Phosphatidylserine synthase 2

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Macromolecule #2: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 2 / Number of copies: 4 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: (7Z,19R,22R)-25-amino-22-hydroxy-16,22-dioxo-17,21,23-trioxa-22la...

MacromoleculeName: (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
type: ligand / ID: 4 / Number of copies: 2 / Formula: RXY
Molecular weightTheoretical: 715.981 Da
Chemical component information

ChemComp-RXY:
(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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration14 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: alpha-fold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93953
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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