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- EMDB-24674: Seipin forms a flexible cage at lipid droplet formation sites -

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Basic information

Entry
Database: EMDB / ID: EMD-24674
TitleSeipin forms a flexible cage at lipid droplet formation sites
Map data
Sample
  • Complex: Seipin; Sei1; Fld1
    • Complex: Seipin dimer
      • Protein or peptide: Seipin
Keywordslipid droplets / lipid droplet formation / complex / endoplasmic reticulum / fat storage / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of sphingolipid biosynthetic process / lipid droplet formation / cortical endoplasmic reticulum / acylglycerol homeostasis / phospholipid homeostasis / lipid droplet organization / protein localization to lipid droplet / regulation of lipid metabolic process / positive regulation of lipid biosynthetic process / lipid droplet ...negative regulation of sphingolipid biosynthetic process / lipid droplet formation / cortical endoplasmic reticulum / acylglycerol homeostasis / phospholipid homeostasis / lipid droplet organization / protein localization to lipid droplet / regulation of lipid metabolic process / positive regulation of lipid biosynthetic process / lipid droplet / lipid metabolic process / intracellular protein localization / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsArlt H / Sui X
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124348 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084210 United States
German Research Foundation (DFG)AR1164/1-1 United States
American Heart AssociationPOST34030308 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Seipin forms a flexible cage at lipid droplet formation sites.
Authors: Henning Arlt / Xuewu Sui / Brayden Folger / Carson Adams / Xiao Chen / Roman Remme / Fred A Hamprecht / Frank DiMaio / Maofu Liao / Joel M Goodman / Robert V Farese / Tobias C Walther /
Abstract: Lipid droplets (LDs) form in the endoplasmic reticulum by phase separation of neutral lipids. This process is facilitated by the seipin protein complex, which consists of a ring of seipin monomers, ...Lipid droplets (LDs) form in the endoplasmic reticulum by phase separation of neutral lipids. This process is facilitated by the seipin protein complex, which consists of a ring of seipin monomers, with a yet unclear function. Here, we report a structure of S. cerevisiae seipin based on cryogenic-electron microscopy and structural modeling data. Seipin forms a decameric, cage-like structure with the lumenal domains forming a stable ring at the cage floor and transmembrane segments forming the cage sides and top. The transmembrane segments interact with adjacent monomers in two distinct, alternating conformations. These conformations result from changes in switch regions, located between the lumenal domains and the transmembrane segments, that are required for seipin function. Our data indicate a model for LD formation in which a closed seipin cage enables triacylglycerol phase separation and subsequently switches to an open conformation to allow LD growth and budding.
History
DepositionAug 11, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0091
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0091
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rsl
  • Surface level: 0.0091
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rsl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24674.png

Downloads & links

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Map

FileDownload / File: emd_24674.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 296 pix.
= 244.2 Å		0.83 Å/pix.
x 296 pix.
= 244.2 Å		0.83 Å/pix.
x 296 pix.
= 244.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0091 / Movie #1: 0.0091
Minimum - Maximum-0.014762914 - 0.0376877
Average (Standard dev.)0.0001796108 (±0.0021997513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 244.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z244.200244.200244.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-0.0150.0380.000

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Supplemental data

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Sample components

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Entire : Seipin; Sei1; Fld1

EntireName: Seipin; Sei1; Fld1
Components
  • Complex: Seipin; Sei1; Fld1
    • Complex: Seipin dimer
      • Protein or peptide: Seipin

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Supramolecule #1: Seipin; Sei1; Fld1

SupramoleculeName: Seipin; Sei1; Fld1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Seipin complex; 10 subunits of monomers (chain A-J) in two alternating conformations
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60 / Organelle: ER / Location in cell: ER-LD junction
Molecular weightTheoretical: 66 KDa

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Supramolecule #2: Seipin dimer

SupramoleculeName: Seipin dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: Dimer of seipin monomers in transmembrane segment conformation A and B (chain A and B). That was used to build the oligomer consisting of 5 dimers (10 monomers).
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60 / Organelle: ER / Location in cell: ER-LD junction

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Macromolecule #1: Seipin

MacromoleculeName: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60
Molecular weightTheoretical: 32.623953 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKINVSRPLQ FLQWSSYIVV AFLIQLLIIL PLSILIYHDF YLRLLPADSS NVVPLNTFNI LNGVQFGTKF FQSIKSIPVG TDLPQTIDN GLSQLIPMRD NMEYKLDLNL QLYCQSKTDH LNLDNLLIDV YRGPGPLLGA PGGSNSKDEK IFHTSRPIVC L ALTDSMSP ...String:
MKINVSRPLQ FLQWSSYIVV AFLIQLLIIL PLSILIYHDF YLRLLPADSS NVVPLNTFNI LNGVQFGTKF FQSIKSIPVG TDLPQTIDN GLSQLIPMRD NMEYKLDLNL QLYCQSKTDH LNLDNLLIDV YRGPGPLLGA PGGSNSKDEK IFHTSRPIVC L ALTDSMSP QEIEQLGPSR LDVYDEEWLN TIRIEDKISL ESSYETISVF LKTEIAQRNL IIHPESGIKF RMNFEQGLRN LM LRKRFLS YIIGISIFHC IICVLFFITG CTAFIFVRKG QEKSKKHS

UniProtKB: Seipin

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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

Concentration3.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris
5.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12655 / Average exposure time: 1.9 sec. / Average electron dose: 54.59 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 49028
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7rsl:
Seipin forms a flexible cage at lipid droplet formation sites

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