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- PDB-6ds5: Cryo EM structure of human SEIPIN -

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Basic information

Entry
Database: PDB / ID: 6ds5
TitleCryo EM structure of human SEIPIN
ComponentsSeipin
KeywordsLIPID BINDING PROTEIN / Lipid droplets / adipogenesis
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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsYan, R.H. / Qian, H.W. / Yan, N. / Yang, H.Y.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2018 / Release: Oct 24, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 24, 2018Structure modelrepositoryInitial release
1.1Oct 31, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Seipin
B: Seipin
C: Seipin
D: Seipin
E: Seipin
F: Seipin
G: Seipin
H: Seipin
I: Seipin
J: Seipin
K: Seipin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)508,37633
Polyers503,50911
Non-polymers4,86722
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)28700
ΔGint (kcal/M)-111
Surface area (Å2)92960
MethodPISA

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Components

#1: Protein/peptide
Seipin / / Bernardinelli-Seip congenital lipodystrophy type 2 protein


Mass: 45773.559 Da / Num. of mol.: 11 / Source: (gene. exp.) Homo sapiens (human) / Gene: BSCL2 / Production host: Homo sapiens (human) / References: UniProt: Q96G97
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 22 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SEIPIN / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 99281 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01014311
ELECTRON MICROSCOPYf_angle_d1.42019503
ELECTRON MICROSCOPYf_dihedral_angle_d14.7888437
ELECTRON MICROSCOPYf_chiral_restr0.0682321
ELECTRON MICROSCOPYf_plane_restr0.0082442

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