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- PDB-11bb: Lipid droplet biogenesis by the lipid droplet assembly complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 11bb
TitleLipid droplet biogenesis by the lipid droplet assembly complex
Components
  • Lipid droplet assembly factor 1-A
  • Seipin
KeywordsMEMBRANE PROTEIN / Complex / endoplasmic reticulum / lipid droplet
Function / homology
Function and homology information


lipid droplet formation / lipid storage / lipid droplet organization / lipid metabolic process / lipid droplet / endoplasmic reticulum membrane
Similarity search - Function
Lipid droplet assembly factor 1 / Promethin / Seipin family / Putative adipose-regulatory protein (Seipin)
Similarity search - Domain/homology
berardinelli-Seip congenital lipodystrophy 2 (Seipin) L homeolog isoform X1 / Lipid droplet assembly factor 1-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 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 lipid droplet assembly complex
Authors: Pedro, C.M. / Siyoung, K. / Yohannes, A. / Gregory, V. / Tobias, W. / Robert, F.
History
DepositionFeb 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / 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
L: Lipid droplet assembly factor 1-A
M: Lipid droplet assembly factor 1-A
N: Lipid droplet assembly factor 1-A
O: Lipid droplet assembly factor 1-A
P: Lipid droplet assembly factor 1-A
Q: Lipid droplet assembly factor 1-A
R: Lipid droplet assembly factor 1-A
K: Seipin
S: Lipid droplet assembly factor 1-A
T: Lipid droplet assembly factor 1-A
U: Lipid droplet assembly factor 1-A
V: Lipid droplet assembly factor 1-A


Theoretical massNumber of molelcules
Total (without water)424,66222
Polymers424,66222
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: 30341.439 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
#2: Protein
Lipid droplet assembly factor 1-A / Promethin-A / Transmembrane protein 159-A


Mass: 8264.156 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ldaf1-a, tmem159-a / Production host: Homo sapiens (human) / References: UniProt: Q68F33
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: Xenopus laevis (African clawed frog)
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: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 573725 / Symmetry type: POINT

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