+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24674 | ||||||||||||||||||
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Title | Seipin forms a flexible cage at lipid droplet formation sites | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | lipid 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 / : / 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 species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||||||||||||||
Authors | Arlt H / Sui X | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24674.map.gz | 77 MB | EMDB map data format | |
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Header (meta data) | emd-24674-v30.xml emd-24674.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_24674.png | 158.6 KB | ||
Filedesc metadata | emd-24674.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24674 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24674 | HTTPS FTP |
-Validation report
Summary document | emd_24674_validation.pdf.gz | 522.5 KB | Display | EMDB validaton report |
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Full document | emd_24674_full_validation.pdf.gz | 522.1 KB | Display | |
Data in XML | emd_24674_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_24674_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24674 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24674 | HTTPS FTP |
-Related structure data
Related structure data | 7rslMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24674.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Seipin; Sei1; Fld1
Entire | Name: Seipin; Sei1; Fld1 |
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Components |
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-Supramolecule #1: Seipin; Sei1; Fld1
Supramolecule | Name: 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 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60 / Organelle: ER / Location in cell: ER-LD junction |
Molecular weight | Theoretical: 66 KDa |
-Supramolecule #2: Seipin dimer
Supramolecule | Name: 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). |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60 / Organelle: ER / Location in cell: ER-LD junction |
-Macromolecule #1: Seipin
Macromolecule | Name: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: HAY60 |
Molecular weight | Theoretical: 32.623953 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7rsl: |