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- EMDB-62506: Cryo-EM structure of PSS1 with calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-62506
TitleCryo-EM structure of PSS1 with calcium
Map data
Sample
  • Complex: cryoEM structure of PSS1 dimer
    • Protein or peptide: Phosphatidylserine synthase 1
  • Ligand: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: DODECANE
  • Ligand: TETRADECANE
  • Ligand: CALCIUM ION
  • Ligand: Phosphatidylinositol
Keywordsphosphatidylserine synthase / ER membrane protein / integral membrane protein / transmembrane enzyme / PS / MEMBRANE PROTEIN
Function / homology
Function and homology information


L-serine-phosphatidylethanolamine phosphatidyltransferase / L-serine-phosphatidylethanolamine phosphatidyltransferase activity / L-serine-phosphatidylcholine 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsNing Y / Yu J / Ge J
Funding support1 items
OrganizationGrant numberCountry
Other governmentLG-QS-202203-05; 22PJ1410300;32471016
CitationJournal: Cell Discov / Year: 2025
Title: Structural basis for catalytic mechanism of human phosphatidylserine synthase 1.
Authors: Yingjie Ning / Ruisheng Xu / Jie Yu / Jingpeng Ge /
History
DepositionNov 26, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62506.png

Downloads & links

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Map

FileDownload / File: emd_62506.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.576
Minimum - Maximum-3.078706 - 4.291337
Average (Standard dev.)0.0023974003 (±0.0929485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62506_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62506_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryoEM structure of PSS1 dimer

EntireName: cryoEM structure of PSS1 dimer
Components
  • Complex: cryoEM structure of PSS1 dimer
    • Protein or peptide: Phosphatidylserine synthase 1
  • Ligand: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: DODECANE
  • Ligand: TETRADECANE
  • Ligand: CALCIUM ION
  • Ligand: Phosphatidylinositol

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Supramolecule #1: cryoEM structure of PSS1 dimer

SupramoleculeName: cryoEM structure of PSS1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phosphatidylserine synthase 1

MacromoleculeName: Phosphatidylserine synthase 1 / 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: 55.590383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASCVGSRTL SKDDVNYKMH FRMINEQQVE DITIDFFYRP HTITLLSFTI VSLMYFAFTR DDSVPEDNIW RGILSVIFFF LIISVLAFP NGPFTRPHPA LWRMVFGLSV LYFLFLVFLL FLNFEQVKSL MYWLDPNLRY ATREADVMEY AVNCHVITWE R IISHFDIF ...String:
MASCVGSRTL SKDDVNYKMH FRMINEQQVE DITIDFFYRP HTITLLSFTI VSLMYFAFTR DDSVPEDNIW RGILSVIFFF LIISVLAFP NGPFTRPHPA LWRMVFGLSV LYFLFLVFLL FLNFEQVKSL MYWLDPNLRY ATREADVMEY AVNCHVITWE R IISHFDIF AFGHFWGWAM KALLIRSYGL CWTISITWEL TELFFMHLLP NFAECWWDQV ILDILLCNGG GIWLGMVVCR FL EMRTYHW ASFKDIHTTT GKIKRAVLQF TPASWTYVRW FDPKSSFQRV AGVYLFMIIW QLTELNTFFL KHIFVFQASH PLS WGRILF IGGITAPTVR QYYAYLTDTQ CKRVGTQCWV FGVIGFLEAI VCIKFGQDLF SKTQILYVVL WLLCVAFTTF LCLY GMIWY AEHYGHREKT YSECEDGTYS PEISWHHRKG TKGSEDSPPK HAGNNESHSS RRRNRHSKSK VTNGVGKK

UniProtKB: Phosphatidylserine synthase 1

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Macromolecule #2: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

MacromoleculeName: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PSF
Molecular weightTheoretical: 455.437 Da
Chemical component information

ChemComp-PSF:
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

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Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 10 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #4: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 4 / Number of copies: 2 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #5: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 5 / Number of copies: 2 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 7 / Number of copies: 2 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 455789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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