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

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Basic information

Entry
Database: EMDB / ID: 8909
TitleCryo EM structure of human SEIPIN
Map dataCryo EM structure of human SEIPIN, primary map
SampleSEIPIN:
Seipin / ligand
Function / homologyPutative adipose-regulatory protein (Seipin) / Seipin family / lipid storage / lipid droplet organization / integral component of endoplasmic reticulum membrane / fat cell differentiation / negative regulation of lipid catabolic process / lipid catabolic process / positive regulation of cold-induced thermogenesis / Seipin
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsYan RH / Qian HW / Yan N / Yang HY
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.
Validation ReportPDB-ID: 6ds5

SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2018 / Header (metadata) release: Jul 18, 2018 / Map release: Oct 24, 2018 / Last update: Oct 31, 2018

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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

Downloads & links

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Map

Fileemd_8909.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
0.88 Å/pix.
= 316.8 Å
360 pix
0.88 Å/pix.
= 316.8 Å
360 pix
0.88 Å/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
Contour Level:0.05 (by author), 0.1 (movie #1):
Minimum - Maximum-0.2975248 - 0.49468955
Average (Standard dev.)0.00058398757 (0.013175286)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 3

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Component #1: cellular-component, SEIPIN

Cellular-componentName: SEIPIN / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Seipin

ProteinName: Seipin / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 45.773559 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 22 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 10 mg/ml / pH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 99281
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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