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- PDB-7oxr: Cryo-EM structure of yeast Sei1 with locking helix deletion -

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Basic information

Entry
Database: PDB / ID: 7oxr
TitleCryo-EM structure of yeast Sei1 with locking helix deletion
ComponentsBJ4_G0032880.mRNA.1.CDS.1
KeywordsMEMBRANE PROTEIN / Lipid droplet formation / lipid binding / seipin
Function / homologySEI1 isoform 1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United Kingdom, 8items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
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Revision 1.1Oct 20, 2021Group: Data collection / Database references
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Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
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Assembly

Deposited unit
A: BJ4_G0032880.mRNA.1.CDS.1
B: BJ4_G0032880.mRNA.1.CDS.1
C: BJ4_G0032880.mRNA.1.CDS.1
D: BJ4_G0032880.mRNA.1.CDS.1
E: BJ4_G0032880.mRNA.1.CDS.1
F: BJ4_G0032880.mRNA.1.CDS.1
G: BJ4_G0032880.mRNA.1.CDS.1
H: BJ4_G0032880.mRNA.1.CDS.1
I: BJ4_G0032880.mRNA.1.CDS.1
J: BJ4_G0032880.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)354,62610
Polymers354,62610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21880 Å2
ΔGint-112 kcal/mol
Surface area72580 Å2

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Components

#1: Protein
BJ4_G0032880.mRNA.1.CDS.1 / HLJ1_G0030540.mRNA.1.CDS.1 / Seipin / Y55_G0030470.mRNA.1.CDS.1


Mass: 35462.590 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS4180, PACBIOSEQ_LOCUS4257, PACBIOSEQ_LOCUS4334, SCNYR20_0004039900, SCP684_0004039500
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUS7
Has protein modificationY

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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: homodecamer of Sei1 with locking helix deletion / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 59.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C10 (10 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260532 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313900
ELECTRON MICROSCOPYf_angle_d0.50818810
ELECTRON MICROSCOPYf_dihedral_angle_d4.2831800
ELECTRON MICROSCOPYf_chiral_restr0.0432190
ELECTRON MICROSCOPYf_plane_restr0.0072420

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