6DS5 | pdb_00006ds5

Cryo EM structure of human SEIPIN

• PDB DOI: https://doi.org/10.2210/pdb6DS5/pdb
• EM Map EMD-8909: EMDB EMDataResource

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2018-06-13 Released: 2018-10-24 
• Deposition Author(s): Yan, R.H., Qian, H.W., Yan, N., Yang, H.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Human SEIPIN Binds Anionic Phospholipids.

Yan, R., Qian, H., Lukmantara, I., Gao, M., Du, X., Yan, N., Yang, H.

(2018) Dev Cell 47: 248-256.e4

• PubMed: 30293840 
• DOI: https://doi.org/10.1016/j.devcel.2018.09.010
• Primary Citation Related Structures: 
  6DS5


• PubMed 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 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.

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Organizational Affiliation: 
• Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. Electronic address: [e-mail].
School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW 2052, Australia.
Laboratory of Lipid Metabolism, Hebei Medical University, Shijiazhuang, Hebei 050017, China.
Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA. Electronic address: [e-mail].
School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW 2052, Australia. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C11  (Explore in 3D)
Global Stoichiometry: Homo 11-mer - A11 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 508.18 kDa 
• Atom Count: 13,970 
• Modeled Residue Count: 1,760 
• Deposited Residue Count: 4,499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seipin	A, B, C, D, E, F, G, H, I, J, K	409	Homo sapiens	Mutation(s): 0  Gene Names: BSCL2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96G97 (Homo sapiens) Explore Q96G97  Go to UniProtKB:  Q96G97
PHAROS:  Q96G97 GTEx:  ENSG00000168000
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q96G97-2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, M, N, O, P, Q, R, S, T, U, V	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Yan, R.H., Qian, H.W., Yan, N., Yang, H.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0502004
National Health and Medical Research Council (NHMRC, Australia)	Australia	1078117

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2018-10-31
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2025-05-28
  Changes: Data collection