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- PDB-9c8d: mouse Seipin/Adig complex -

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Basic information

Entry
Database: PDB / ID: 9c8d
Titlemouse Seipin/Adig complex
Components
  • Adipogenin
  • Seipin
KeywordsMEMBRANE PROTEIN / seipin / adipogenin / lipid droplets / adipose
Function / homology
Function and homology information


lipid droplet formation / white fat cell differentiation / positive regulation of fat cell differentiation / brown fat cell differentiation / lipid droplet / phospholipid binding / lipid metabolic process / spermatogenesis / endoplasmic reticulum membrane / nucleus ...lipid droplet formation / white fat cell differentiation / positive regulation of fat cell differentiation / brown fat cell differentiation / lipid droplet / phospholipid binding / lipid metabolic process / spermatogenesis / endoplasmic reticulum membrane / nucleus / membrane / cytoplasm
Similarity search - Function
Adipogenin / Adipogenin / Seipin family / Putative adipose-regulatory protein (Seipin)
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLi, C. / Han, Y. / Wynn, R.M. / Chen, Z. / Scherer, P.E.
Funding support United States, 5items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Nov 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
L: Seipin
M: Adipogenin
N: Adipogenin
O: Adipogenin
P: Adipogenin
Q: Adipogenin
R: Adipogenin
S: Adipogenin
T: Adipogenin
U: Adipogenin
V: Adipogenin
W: Adipogenin
X: Adipogenin


Theoretical massNumber of molelcules
Total (without water)741,12624
Polymers741,12624
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Seipin


Mass: 50993.406 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bscl2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A0R4J225
#2: Protein
Adipogenin / Small adipocyte factor 1 / SMAF-1


Mass: 10767.105 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adig, Smaf1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8R400
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Seipin/Adig complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.7 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32123 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322056
ELECTRON MICROSCOPYf_angle_d0.5530036
ELECTRON MICROSCOPYf_dihedral_angle_d4.6182952
ELECTRON MICROSCOPYf_chiral_restr0.0413480
ELECTRON MICROSCOPYf_plane_restr0.0043672

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