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- PDB-6mlu: Cryo-EM structure of lipid droplet formation protein Seipin/BSCL2 -

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Basic information

Entry
Database: PDB / ID: 6mlu
TitleCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
ComponentsSeipin
KeywordsMEMBRANE PROTEIN / Lipid storage / Lipid droplet formation / lipodystrophy
Function / homology
Function and homology information


positive regulation of axon extension involved in regeneration / diacylglycerol metabolic process / regulation of triglyceride metabolic process / lipid droplet formation / phosphatidic acid metabolic process / : / regulation of lipid storage / regulation of lipid biosynthetic process / positive regulation of lipid storage / lipid storage ...positive regulation of axon extension involved in regeneration / diacylglycerol metabolic process / regulation of triglyceride metabolic process / lipid droplet formation / phosphatidic acid metabolic process / : / regulation of lipid storage / regulation of lipid biosynthetic process / positive regulation of lipid storage / lipid storage / lipid droplet organization / endoplasmic reticulum calcium ion homeostasis / lipid biosynthetic process / fatty acid beta-oxidation / response to starvation / lipid droplet / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Seipin family / Putative adipose-regulatory protein (Seipin)
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSui, X. / Arlt, H. / Liao, M. / Walther, C.T. / Farese, V.R.
Funding support United States, Germany, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM123089 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM124348-01 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM097194 United States
American Heart Association18POST34030308 United States
German Research Foundation (DFG)AR1164/1-1 Germany
CitationJournal: J Cell Biol / Year: 2018
Title: Cryo-electron microscopy structure of the lipid droplet-formation protein seipin.
Authors: Xuewu Sui / Henning Arlt / Kelly P Brock / Zon Weng Lai / Frank DiMaio / Debora S Marks / Maofu Liao / Robert V Farese / Tobias C Walther /
Abstract: Metabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic ...Metabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic reticulum (ER) bilayer is poorly understood, but the ER protein seipin is essential to this process. In this study, we report a cryo-electron microscopy structure and functional characterization of seipin. The structure reveals a ring-shaped dodecamer with the luminal domain of each monomer resolved at ∼4.0 Å. Each luminal domain monomer exhibits two distinctive features: a hydrophobic helix (HH) positioned toward the ER bilayer and a β-sandwich domain with structural similarity to lipid-binding proteins. This structure and our functional testing in cells suggest a model in which seipin oligomers initially detect forming LDs in the ER via HHs and subsequently act as membrane anchors to enable lipid transfer and LD growth.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
A: Seipin
B: Seipin


Theoretical massNumber of molelcules
Total (without water)87,9142
Polymers87,9142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Negative staining electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area17750 Å2

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Components

#1: Protein Seipin /


Mass: 43957.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Seipin, CG9904 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V3X4

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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: cryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 43 kDa/nm / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28a
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Protein sample was monodisperse.
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 58 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D12 (2x12 fold dihedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22383 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052584
ELECTRON MICROSCOPYf_angle_d1.0183502
ELECTRON MICROSCOPYf_dihedral_angle_d4.3831574
ELECTRON MICROSCOPYf_chiral_restr0.064388
ELECTRON MICROSCOPYf_plane_restr0.007442

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