6M49 | pdb_00006m49

cryo-EM structure of Scap/Insig complex in the present of 25-hydroxyl cholesterol.

• PDB DOI: https://doi.org/10.2210/pdb6M49/pdb
• EM Map EMD-30074: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-03-06 Released: 2021-01-20 
• Deposition Author(s): Yan, R., Cao, P., Song, W., Qian, H., Du, X., Coates, H.W., Zhao, X., Li, Y., Gao, S., Gong, X., Liu, X., Sui, J., Lei, J., Yang, H., Brown, A.J., Zhou, Q., Yan, C., Yan, N.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A structure of human Scap bound to Insig-2 suggests how their interaction is regulated by sterols.

Yan, R., Cao, P., Song, W., Qian, H., Du, X., Coates, H.W., Zhao, X., Li, Y., Gao, S., Gong, X., Liu, X., Sui, J., Lei, J., Yang, H., Brown, A.J., Zhou, Q., Yan, C., Yan, N.

(2021) Science 371

• PubMed: 33446483 
• DOI: https://doi.org/10.1126/science.abb2224
• Primary Citation Related Structures: 
  6M49


• PubMed Abstract: 
  

  The sterol regulatory element-binding protein (SREBP) pathway controls cellular homeostasis of sterols. The key players in this pathway, Scap and Insig-1 and -2, are membrane-embedded sterol sensors. The 25-hydroxycholesterol (25HC)-dependent association of Scap and Insig acts as the master switch for the SREBP pathway. Here, we present cryo-electron microscopy analysis of the human Scap and Insig-2 complex in the presence of 25HC, with the transmembrane (TM) domains determined at an average resolution of 3.7 angstrom. The sterol-sensing domain in Scap and all six TMs in Insig-2 were resolved. A 25HC molecule is sandwiched between the S4 to S6 segments in Scap and TMs 3 and 4 in Insig-2 in the luminal leaflet of the membrane. Unwinding of the middle of the Scap-S4 segment is crucial for 25HC binding and Insig association.

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Organizational Affiliation: 
• Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China.
State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia.
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
National Institute of Biological Sciences (NIBS), Beijing 102206, China.
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. [e-mail] [e-mail].
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.45 kDa 
• Atom Count: 3,098 
• Modeled Residue Count: 420 
• Deposited Residue Count: 797 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-induced gene 2 protein	A	225	Homo sapiens	Mutation(s): 3  Gene Names: INSIG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5U4 (Homo sapiens) Explore Q9Y5U4  Go to UniProtKB:  Q9Y5U4
PHAROS:  Q9Y5U4 GTEx:  ENSG00000125629

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sterol regulatory element-binding protein cleavage-activating protein,Sterol regulatory element-binding protein cleavage-activating protein	B	572	Homo sapiens	Mutation(s): 0  Gene Names: SCAP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12770 (Homo sapiens) Explore Q12770  Go to UniProtKB:  Q12770
PHAROS:  Q12770 GTEx:  ENSG00000114650

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC3 (Subject of Investigation/LOI)	C [auth A]	25-HYDROXYCHOLESTEROL C27 H46 O2 INBGSXNNRGWLJU-ZHHJOTBYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 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: 2021-01-20 
Deposition Author(s): Yan, R., Cao, P., Song, W., Qian, H., Du, X., Coates, H.W., Zhao, X., Li, Y., Gao, S., Gong, X., Liu, X., Sui, J., Lei, J., Yang, H., Brown, A.J., Zhou, Q., Yan, C., Yan, N.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2021-03-17
  Changes: Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references
• Version 1.4: 2025-06-25
  Changes: Data collection, Structure summary