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

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Basic information

Entry
Database: PDB / ID: 7rsl
TitleSeipin forms a flexible cage at lipid droplet formation sites
ComponentsSeipin
KeywordsMEMBRANE PROTEIN / lipid droplets / lipid droplet formation / complex / endoplasmic reticulum / fat storage
Function / homology
Function and homology information


negative regulation of sphingolipid biosynthetic process / lipid droplet formation / : / protein localization => GO:0008104 / cortical endoplasmic reticulum / lipid droplet organization / positive regulation of lipid biosynthetic process / lipid metabolic process / endoplasmic reticulum / identical protein binding
Similarity search - Function
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsArlt, H. / Sui, X. / Folger, B. / Adams, C. / Chen, X. / Remme, R. / Hamprecht, F.A. / DiMaio, F. / Liao, M. / Goodman, J.M. ...Arlt, H. / Sui, X. / Folger, B. / Adams, C. / Chen, X. / Remme, R. / Hamprecht, F.A. / DiMaio, F. / Liao, M. / Goodman, J.M. / Farese Jr, R.V. / Walther, T.C.
Funding support United States, 5items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Database references / Category: citation / citation_author
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Revision 1.3Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Seipin
B: Seipin
G: Seipin
H: Seipin
E: Seipin
F: Seipin
I: Seipin
J: Seipin
C: Seipin
D: Seipin


Theoretical massNumber of molelcules
Total (without water)326,24010
Polymers326,24010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Negative stain and cryoEM microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28080 Å2
ΔGint-175 kcal/mol
Surface area113950 Å2

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Components

#1: Protein
Seipin / Few lipid droplets protein 1


Mass: 32623.953 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: HAY60 / Gene: SEI1, FLD1, YLR404W / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): HAY60 / References: UniProt: Q06058

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Seipin; Sei1; Fld1COMPLEXSeipin complex; 10 subunits of monomers (chain A-J) in two alternating conformationsall0RECOMBINANT
2Seipin dimerCOMPLEXDimer 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).all1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.33 MDaNO
210.066 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellular locationOrganelle
21Saccharomyces cerevisiae (brewer's yeast)4932HAY60ER-LD junctionER
32Saccharomyces cerevisiae (brewer's yeast)4932HAY60ER-LD junctionER
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTris1
35 mMmagnesium chlorideMgCl21
SpecimenConc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.9 sec. / Electron dose: 54.59 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12655

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Processing

EM software
IDNameVersionCategory
2SerialEM3.6image acquisition
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 49028 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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