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- EMDB-45302: mouse Seipin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45302
Titlemouse Seipin complex
Map datamouse seipin complex
Sample
  • Complex: Seipin complex
    • Protein or peptide: Seipin
Keywordsseipin / lipid droplets / adipose / MEMBRANE PROTEIN
Function / homologySeipin family / Putative adipose-regulatory protein (Seipin) / lipid droplet formation / lipid droplet / phospholipid binding / lipid metabolic process / endoplasmic reticulum membrane / Seipin
Function and homology information
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLi C / Han Y / Wynn RM / Chen Z / Scherer PE
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RC2-DK118620 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01- DK55758 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK099110 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK127274 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK131537 United States
CitationJournal: Science / Year: 2025
Title: Adipogenin promotes the development of lipid droplets by binding a dodecameric seipin complex.
Authors: Chao Li / Xue-Nan Sun / Jan-Bernd Funcke / Lauri Vanharanta / Xavier Prasanna / Kaitlynn Gov / Yan Li / Megan Virostek / Chanmin Joung / Nolwenn Joffin / Kristiina Kanerva / Abel Szkalisity ...Authors: Chao Li / Xue-Nan Sun / Jan-Bernd Funcke / Lauri Vanharanta / Xavier Prasanna / Kaitlynn Gov / Yan Li / Megan Virostek / Chanmin Joung / Nolwenn Joffin / Kristiina Kanerva / Abel Szkalisity / Waldemar Kulig / Leon Straub / Shiuhwei Chen / Joselin Velasco / Ayanna Cobb / Davide La Padula / May-Yun Wang / Toshiharu Onodera / Csaba Vörös / Dae-Seok Kim / Min Kim / Oleg Varlamov / Yang Li / Chen Liu / Andrea R Nawrocki / Shangang Zhao / Da Young Oh / Zhao V Wang / Ruth Gordillo / Joel M Goodman / R Max Wynn / W Mike Henne / Ilpo Vattulainen / Yan Han / Elina Ikonen / Philipp E Scherer /
Abstract: The microprotein adipogenin (Adig) is predominantly expressed in adipose tissues. Here, we found that Adig interacts with seipin to form a stable, rigid complex. We present the structure of the ...The microprotein adipogenin (Adig) is predominantly expressed in adipose tissues. Here, we found that Adig interacts with seipin to form a stable, rigid complex. We present the structure of the seipin-Adig complex at an overall resolution of ~3.0 angstroms. The structure revealed that mammalian seipin assembles into two distinct oligomeric forms: undecamers and dodecamers. Adig selectively bound to the dodecameric form and enhanced seipin assembly by bridging and stabilizing adjacent subunits. Functionally, this complex promoted lipid droplet development at both early and late stages. In transgenic mice, adipocyte-specific overexpression of Adig increased fat mass and enlarged lipid droplets, whereas Adig deletion disrupted triglyceride accumulation in brown adipose tissues. Thus, Adig can modulate lipid storage through its structural and functional interactions with seipin.
History
DepositionJun 12, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45302.png

Downloads & links

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Map

FileDownload / File: emd_45302.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse seipin complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 320.41 Å		0.83 Å/pix.
x 384 pix.
= 320.41 Å		0.83 Å/pix.
x 384 pix.
= 320.41 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8344 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0018974592 - 2.0808237
Average (Standard dev.)0.0011424852 (±0.025523048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 320.4096 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2 of seipin complex

Fileemd_45302_half_map_1.map
Annotationhalf map 2 of seipin complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 of seipin complex

Fileemd_45302_half_map_2.map
Annotationhalf map 1 of seipin complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Seipin complex

EntireName: Seipin complex
Components
  • Complex: Seipin complex
    • Protein or peptide: Seipin

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Supramolecule #1: Seipin complex

SupramoleculeName: Seipin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Seipin

MacromoleculeName: Seipin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.993406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGRWSHPQF EKIHQRREAG ARETCRDQIK GSDKDEEPSA ALSHGQGYRP CGRPARNSKP EAGARPPAVP IMVNDPPVPA LLWAQEVGH VLAGRARRLM LQFGVLFCTI LLLLWVSVFL YGSFYYSYMP TVSHLSPVHF HYRTDCDSST ASLCSFPVAN V SLAKSGRD ...String:
MSGRWSHPQF EKIHQRREAG ARETCRDQIK GSDKDEEPSA ALSHGQGYRP CGRPARNSKP EAGARPPAVP IMVNDPPVPA LLWAQEVGH VLAGRARRLM LQFGVLFCTI LLLLWVSVFL YGSFYYSYMP TVSHLSPVHF HYRTDCDSST ASLCSFPVAN V SLAKSGRD RVLMYGQPYR VTLELELPES PVNQDLGMFL VTVSCYTRGG RIISTSSRSV MLHYRSQLLQ VLDTLLFSSL LL FGFAEQK QLLEVELYSD YRENSYVPTT GAIIEIHSKR IQMYGAYLRI HAHFTGLRYL LYNFPMTCAF VGVASNFTFL SVI VLFSYM QWVWGAVWPR HRFSLQVNIR QRDNSHHGAP RRISRHQPGQ ESTQQSDVTE DGESPEDPSG TEGQLSEEEK PEKR PLNGE EEQEPEASDG SWEDAALLTE ANPPTSASAS ALAPETLGSL RQRPTCSSS

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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17212
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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