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- PDB-9p9w: Lipid droplet biogenesis by the seipin complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9p9w
TitleLipid droplet biogenesis by the seipin complex
ComponentsSeipin
KeywordsMEMBRANE PROTEIN / Complex / endoplasmic reticulum / lipid droplet
Function / homologySeipin family / Putative adipose-regulatory protein (Seipin) / lipid droplet formation / lipid storage / lipid droplet organization / lipid metabolic process / endoplasmic reticulum membrane / berardinelli-Seip congenital lipodystrophy 2 (Seipin) L homeolog isoform X1
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPedro, C.M. / Siyoung, K. / Yohannes, A. / Gregory, V. / Tobias, W. / Robert, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124348 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Lipid droplet biogenesis by the seipin complex
Authors: Pedro, C.M. / Siyoung, K. / Yohannes, A. / Gregory, V. / Tobias, W. / Robert, F.
History
DepositionJun 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seipin
B: Seipin
C: Seipin
D: Seipin
E: Seipin
F: Seipin
G: Seipin
H: Seipin
I: Seipin
J: Seipin
K: Seipin


Theoretical massNumber of molelcules
Total (without water)423,02511
Polymers423,02511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Seipin


Mass: 38456.801 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: bscl2.L, bscl2, seipin / Production host: Homo sapiens (human) / References: UniProt: A0A1L8GJQ5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Seipin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.29 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topazparticle selectionParticle picking
2cryoSPARC4.7particle selectionClassification
3cryoSPARC4.7particle selectionReconstruction
4PHENIX1.18particle selectionModel refinement
5PHENIX1.21.2_5419model refinement
16cryoSPARC4.73D reconstructionSingle particle
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 646025 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.59 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002614047
ELECTRON MICROSCOPYf_angle_d0.50619041
ELECTRON MICROSCOPYf_chiral_restr0.04292156
ELECTRON MICROSCOPYf_plane_restr0.00382431
ELECTRON MICROSCOPYf_dihedral_angle_d3.95431958

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