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- EMDB-8909: Cryo EM structure of human SEIPIN -

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Basic information

Entry
Database: EMDB / ID: EMD-8909
TitleCryo EM structure of human SEIPIN
Map dataCryo EM structure of human SEIPIN, primary map
Sample
  • Organelle or cellular component: SEIPIN
    • Protein or peptide: Seipin
KeywordsLipid droplets / adipogenesis / LIPID BINDING PROTEIN
Function / homology
Function and homology information


lipid droplet formation / lipid droplet organization / lipid storage / 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
Seipin family / Putative adipose-regulatory protein (Seipin)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYan RH / Qian HW
Funding support China, Australia, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0502004 China
National Health and Medical Research Council (NHMRC, Australia)1078117 Australia
CitationJournal: 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
DepositionJun 13, 2018-
Header (metadata) releaseJul 18, 2018-
Map releaseOct 24, 2018-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ds5
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8909.png

Downloads & links

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Map

FileDownload / File: emd_8909.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM structure of human SEIPIN, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.1
Minimum - Maximum-0.2975248 - 0.49468955
Average (Standard dev.)0.00058398757 (±0.013175286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2980.4950.001

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Supplemental data

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Sample components

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Entire : SEIPIN

EntireName: SEIPIN
Components
  • Organelle or cellular component: SEIPIN
    • Protein or peptide: Seipin

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Supramolecule #1: SEIPIN

SupramoleculeName: SEIPIN / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Seipin

MacromoleculeName: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.773559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Seipin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99281
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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