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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: 9146
TitleCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Map dataCryo-EM structure of lipid droplet formation protein Seipin/BSCL2
Samplecryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy:
Seipin
Function / homologyPutative adipose-regulatory protein (Seipin) / Seipin family / diacylglycerol metabolic process / positive regulation of axon extension involved in regeneration / regulation of triglyceride metabolic process / phosphatidic acid metabolic process / regulation of lipid biosynthetic process / regulation of lipid storage / lipid storage / positive regulation of lipid storage ...Putative adipose-regulatory protein (Seipin) / Seipin family / diacylglycerol metabolic process / positive regulation of axon extension involved in regeneration / regulation of triglyceride metabolic process / phosphatidic acid metabolic process / regulation of lipid biosynthetic process / regulation of lipid storage / lipid storage / positive regulation of lipid storage / endoplasmic reticulum calcium ion homeostasis / lipid biosynthetic process / fatty acid beta-oxidation / response to starvation / endoplasmic reticulum membrane / endoplasmic reticulum / integral component of membrane / Seipin
Function and homology information
SourceDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsSui X / Arlt H / Liao M / Walther CT / Farese VR
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.
Validation ReportPDB-ID: 6mlu

SummaryFull reportAbout validation report
DateDeposition: Sep 28, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Oct 17, 2018 / Last update: Oct 31, 2018

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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
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6mlu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9146.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.033 (by author), 0.033 (movie #1):
Minimum - Maximum-0.07455186 - 0.1342655
Average (Standard dev.)0.00003190383 (0.0073412494)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 deg.

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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Sample components

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Entire cryo-EM protein structure of seipin/BSCL2

EntireName: cryo-EM protein structure of seipin/BSCL2 / Number of components: 2

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Component #1: cellular-component, cryo-EM protein structure of seipin/BSCL2

Cellular-componentName: cryo-EM protein structure of seipin/BSCL2Transmission electron cryomicroscopy
Recombinant expression: No
MassTheoretical: 43 MDa
SourceSpecies: Drosophila melanogaster (fruit fly)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET28a

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Component #2: protein, Seipin

ProteinName: Seipin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.95707 kDa
SourceSpecies: Drosophila melanogaster (fruit fly)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
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
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 58 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D12 (2*12 fold dihedral) / Number of projections: 22383
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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