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- EMDB-9146: Cryo-EM structure of lipid droplet formation protein Seipin/BSCL2 -

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Basic information

Entry
Database: EMDB / ID: EMD-9146
TitleCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Map dataCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Sample
  • Organelle or cellular component: cryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy
    • Protein or peptide: Seipin
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSui X / Arlt H / Liao M / Walther CT / Farese VR
Funding support United States, Germany, 6 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) 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)1R01GM123089 United States
American Heart Association18POST34030308 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM097194 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, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mlu
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mlu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9146.png

Downloads & links

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Map

FileDownload / File: emd_9146.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.07455186 - 0.1342655
Average (Standard dev.)0.0000319038 (±0.0073412494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0750.1340.000

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Supplemental data

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Additional map: Cryo-EM structure of lipid droplet formation protein Seipin/BSCL2

Fileemd_9146_additional.map
AnnotationCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryo-EM protein structure of seipin/BSCL2

EntireName: cryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy
Components
  • Organelle or cellular component: cryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy
    • Protein or peptide: Seipin

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Supramolecule #1: cryo-EM protein structure of seipin/BSCL2

SupramoleculeName: cryo-EM protein structure of seipin/BSCL2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 43 kDa/nm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a

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Macromolecule #1: Seipin

MacromoleculeName: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 43.95707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGNILLRLIV FALDPLGLGR RFLIRPAVNL GWNVYDRVRS KADEKVGTVR ELVLRLGLIA FAVVLIIWLA VFMYAAFYYV YMPAISHTR PVHMQFKTCL ETSTPCTFPH AHVSLTKKQQ LLMVGQAYKV IVNIDMPESP QNLELGMFMV CAEMRDYDSM L RGHSCRSA ...String:
MGNILLRLIV FALDPLGLGR RFLIRPAVNL GWNVYDRVRS KADEKVGTVR ELVLRLGLIA FAVVLIIWLA VFMYAAFYYV YMPAISHTR PVHMQFKTCL ETSTPCTFPH AHVSLTKKQQ LLMVGQAYKV IVNIDMPESP QNLELGMFMV CAEMRDYDSM L RGHSCRSA MMRYRSPLIR MISTWVLSPL YVLGWKEEFQ QVPVEIFSRY LEERQHPITD VYVEIQSQKI QFYTVTLHIV AD FTGLRYI MFNWPVLSAI VAISTNLFFI LVVFLLSWYH WSDAKWLHSV QIKYARLTKS LEPGVIHSKA SSLRDDDDDL VAY SDKSDI ADVGGDTLSD VDADDLVLVK KSRSGKRESP DALRKRPTKK TTADHAAALE HHHHHH

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3
DetailsProtein sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D12 (2x12 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22383
FSC plot (resolution estimation)

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