+Open data
-Basic information
Entry | Database: PDB / ID: 7oxr | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of yeast Sei1 with locking helix deletion | |||||||||||||||||||||||||||
Components | BJ4_G0032880.mRNA.1.CDS.1 | |||||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Lipid droplet formation / lipid binding / seipin | |||||||||||||||||||||||||||
Function / homology | SEI1 isoform 1 Function and homology information | |||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||
Authors | Deme, J.C. / Lea, S.M. | |||||||||||||||||||||||||||
Funding support | United Kingdom, 8items
| |||||||||||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oxr.cif.gz | 312.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7oxr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oxr_validation.pdf.gz | 740.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7oxr_full_validation.pdf.gz | 755.9 KB | Display | |
Data in XML | 7oxr_validation.xml.gz | 60.3 KB | Display | |
Data in CIF | 7oxr_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/7oxr ftp://data.pdbj.org/pub/pdb/validation_reports/ox/7oxr | HTTPS FTP |
-Related structure data
Related structure data | 13104MC 7oxpC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C10 (10 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260532 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|