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- EMDB-13103: Cryo-EM structure of yeast Sei1 -

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Basic information

Entry
Database: EMDB / ID: EMD-13103
TitleCryo-EM structure of yeast Sei1
Map data
Sample
  • Complex: homodecamer of Sei1
    • Protein or peptide: BJ4_G0032880.mRNA.1.CDS.1,BJ4_G0032880.mRNA.1.CDS.1
Function / homologySEI1 isoform 1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDeme JC / Lea SM
Funding support United Kingdom, 8 items
OrganizationGrant numberCountry
Wellcome Trust208361/Z/17/Z United Kingdom
Wellcome Trust219477/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P01948X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002517/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S009213/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018375/1 United Kingdom
Wellcome Trust202642/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex.
Authors: Yoel A Klug / Justin C Deme / Robin A Corey / Mike F Renne / Phillip J Stansfeld / Susan M Lea / Pedro Carvalho /
Abstract: Lipid droplets (LDs) are universal lipid storage organelles with a core of neutral lipids, such as triacylglycerols, surrounded by a phospholipid monolayer. This unique architecture is generated ...Lipid droplets (LDs) are universal lipid storage organelles with a core of neutral lipids, such as triacylglycerols, surrounded by a phospholipid monolayer. This unique architecture is generated during LD biogenesis at endoplasmic reticulum (ER) sites marked by Seipin, a conserved membrane protein mutated in lipodystrophy. Here structural, biochemical and molecular dynamics simulation approaches reveal the mechanism of LD formation by the yeast Seipin Sei1 and its membrane partner Ldb16. We show that Sei1 luminal domain assembles a homooligomeric ring, which, in contrast to other Seipins, is unable to concentrate triacylglycerol. Instead, Sei1 positions Ldb16, which concentrates triacylglycerol within the Sei1 ring through critical hydroxyl residues. Triacylglycerol recruitment to the complex is further promoted by Sei1 transmembrane segments, which also control Ldb16 stability. Thus, we propose that LD assembly by the Sei1/Ldb16 complex, and likely other Seipins, requires sequential triacylglycerol-concentrating steps via distinct elements in the ER membrane and lumen.
History
DepositionJun 22, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oxp
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oxp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13103.png

Downloads & links

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Map

FileDownload / File: emd_13103.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.14141268 - 0.24345995
Average (Standard dev.)7.333779e-05 (±0.0041958583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 355.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z355.104355.104355.104
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.1410.2430.000

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Supplemental data

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Mask #1

Fileemd_13103_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_13103_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 1

Fileemd_13103_half_map_1.map
Annotationunfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 2

Fileemd_13103_half_map_2.map
Annotationunfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homodecamer of Sei1

EntireName: homodecamer of Sei1
Components
  • Complex: homodecamer of Sei1
    • Protein or peptide: BJ4_G0032880.mRNA.1.CDS.1,BJ4_G0032880.mRNA.1.CDS.1

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Supramolecule #1: homodecamer of Sei1

SupramoleculeName: homodecamer of Sei1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: BJ4_G0032880.mRNA.1.CDS.1,BJ4_G0032880.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0032880.mRNA.1.CDS.1,BJ4_G0032880.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.664125 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 QEKSKKHSGR RIPGLINGGG GGGDYKDHDG DYKDHDIDYK DDD DK

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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) / Average electron dose: 48.0 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: C10 (10 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234898
FSC plot (resolution estimation)

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