+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8909 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo EM structure of human SEIPIN | |||||||||
Map data | Cryo EM structure of human SEIPIN, primary map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information lipid droplet formation / : / lipid storage / lipid droplet organization / fat cell differentiation / negative regulation of lipid catabolic process / lipid catabolic process / lipid droplet / phospholipid binding / positive regulation of cold-induced thermogenesis / endoplasmic reticulum membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Yan RH / Qian HW / Yan N / Yang HY | |||||||||
Funding support | China, Australia, 2 items
| |||||||||
Citation | Journal: Dev Cell / Year: 2018 Title: Human SEIPIN Binds Anionic Phospholipids. Authors: Renhong Yan / Hongwu Qian / Ivan Lukmantara / Mingming Gao / Ximing Du / Nieng Yan / Hongyuan Yang / Abstract: The biogenesis of lipid droplets (LDs) and the development of adipocytes are two key aspects of mammalian fat storage. SEIPIN, an integral membrane protein of the endoplasmic reticulum (ER), plays a ...The biogenesis of lipid droplets (LDs) and the development of adipocytes are two key aspects of mammalian fat storage. SEIPIN, an integral membrane protein of the endoplasmic reticulum (ER), plays a critical role in both LD formation and adipogenesis. The molecular function of SEIPIN, however, has yet to be elucidated. Here, we report the cryogenic electron microscopy structure of human SEIPIN at 3.8 Å resolution. SEIPIN exists as an undecamer, and this oligomerization state is critical for its physiological function. The evolutionarily conserved lumenal domain of SEIPIN forms an eight-stranded β sandwich fold. Both full-length SEIPIN and its lumenal domain can bind anionic phospholipids including phosphatidic acid. Our results suggest that SEIPIN forms a scaffold that helps maintain phospholipid homeostasis and surface tension of the ER. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8909.map.gz | 164.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8909-v30.xml emd-8909.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_8909.png | 75.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8909 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8909 | HTTPS FTP |
-Validation report
Summary document | emd_8909_validation.pdf.gz | 460.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8909_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | emd_8909_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_8909_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8909 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8909 | HTTPS FTP |
-Related structure data
Related structure data | 6ds5MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_8909.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo EM structure of human SEIPIN, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : SEIPIN
Entire | Name: SEIPIN |
---|---|
Components |
|
-Supramolecule #1: SEIPIN
Supramolecule | Name: SEIPIN / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Seipin
Macromolecule | Name: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.773559 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSGRWSHPQF EKVNDPPVPA LLWAQEVGQV LAGRARRLLL QFGVLFCTIL LLLWVSVFLY GSFYYSYMPT VSHLSPVHFY YRTDCDSST TSLCSFPVAN VSLTKGGRDR VLMYGQPYRV TLELELPESP VNQDLGMFLV TISCYTRGGR IISTSSRSVM L HYRSDLLQ ...String: MSGRWSHPQF EKVNDPPVPA LLWAQEVGQV LAGRARRLLL QFGVLFCTIL LLLWVSVFLY GSFYYSYMPT VSHLSPVHFY YRTDCDSST TSLCSFPVAN VSLTKGGRDR VLMYGQPYRV TLELELPESP VNQDLGMFLV TISCYTRGGR IISTSSRSVM L HYRSDLLQ MLDTLVFSSL LLFGFAEQKQ LLEVELYADY RENSYVPTTG AIIEIHSKRI QLYGAYLRIH AHFTGLRYLL YN FPMTCAF IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGPE GQEESTPQSD VTE DGESPE DPSGTEGQLS EEEKPDQQPL SGEEELEPEA SDGSGSWEDA ALLTEANLPA PAPASASAPV LETLGSSEPA GGAL RQRPT CSSS |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99281 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |