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

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Open data


ID or keywords:

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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: To Be Published
Title: Adipogenin Dictates Adipose Tissue Expansion by Facilitating the Assembly of a Dodecameric Seipin Complex
Authors: Li, C. / Sun, X.
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

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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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