[English] 日本語
Yorodumi- PDB-7etw: Cryo-EM structure of Scap/Insig complex in the present of digitonin. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7etw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Scap/Insig complex in the present of digitonin. | |||||||||
Components |
| |||||||||
Keywords | MEMBRANE PROTEIN / sterol sensing / SREBP / Scap / Insig / cholestrol / digitonin | |||||||||
Function / homology | Function and homology information SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / SREBP-SCAP complex / negative regulation of steroid biosynthetic process / regulation of cholesterol biosynthetic process / cellular lipid metabolic process / response to vitamin B3 / sterol binding / SREBP signaling pathway ...SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / SREBP-SCAP complex / negative regulation of steroid biosynthetic process / regulation of cholesterol biosynthetic process / cellular lipid metabolic process / response to vitamin B3 / sterol binding / SREBP signaling pathway / COPII-coated vesicle cargo loading / negative regulation of cholesterol biosynthetic process / regulation of fatty acid biosynthetic process / negative regulation of fatty acid biosynthetic process / positive regulation of cholesterol biosynthetic process / Regulation of cholesterol biosynthesis by SREBP (SREBF) / oxysterol binding / middle ear morphogenesis / inner ear morphogenesis / triglyceride metabolic process / roof of mouth development / cholesterol biosynthetic process / protein sequestering activity / cholesterol metabolic process / response to insulin / ER to Golgi transport vesicle membrane / cellular response to insulin stimulus / unfolded protein binding / response to hypoxia / immune response / Golgi membrane / endoplasmic reticulum membrane / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Yan, R. / Cao, P. / Song, W. / Li, Y. / Wang, T. / Qian, H. / Yan, C. / Yan, N. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: Cell Rep / Year: 2021 Title: Structural basis for sterol sensing by Scap and Insig. Authors: Renhong Yan / Pingping Cao / Wenqi Song / Yaning Li / Tongtong Wang / Hongwu Qian / Chuangye Yan / Nieng Yan / Abstract: The sterol regulatory element-binding protein (SREBP) pathway monitors the cellular cholesterol level through sterol-regulated association between the SREBP cleavage-activating protein (Scap) and the ...The sterol regulatory element-binding protein (SREBP) pathway monitors the cellular cholesterol level through sterol-regulated association between the SREBP cleavage-activating protein (Scap) and the insulin-induced gene (Insig). Despite structural determination of the Scap and Insig-2 complex bound to 25-hydroxycholesterol, the luminal domains of Scap remain unresolved. In this study, combining cryogenic electron microscopy (cryo-EM) analysis and artificial intelligence-facilitated structural prediction, we report the structure of the human Scap/Insig-2 complex purified in digitonin. The luminal domain loop 1 and a co-folded segment in loop 7 of Scap resemble those of the luminal/extracellular domain in NPC1 and related proteins, providing clues to the cholesterol-regulated interaction of loop 1 and loop 7. An additional luminal interface is observed between Scap and Insig. We also show that Scap(D428A), which inhibits SREBP activation even under sterol depletion, exhibits an identical conformation with the wild-type protein when complexed with Insig-2, and its constitutive suppression of the SREBP pathway may also involve a later step in protein trafficking. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7etw.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7etw.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 7etw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7etw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7etw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7etw_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 7etw_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7etw ftp://data.pdbj.org/pub/pdb/validation_reports/et/7etw | HTTPS FTP |
-Related structure data
Related structure data | 31303MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 24749.660 Da / Num. of mol.: 1 / Mutation: C14S, C90S, C215S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INSIG2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9Y5U4 | ||
---|---|---|---|
#2: Protein | Mass: 81863.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCAP, KIAA0199, PSEC0227 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q12770 | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | ChemComp-AJP / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Scap and Insig complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S |
Buffer solution | pH: 8 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252929 / Symmetry type: POINT |