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- EMDB-30074: cryo-EM structure of Scap/Insig complex in the present of 25-hydr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30074 | |||||||||
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Title | cryo-EM structure of Scap/Insig complex in the present of 25-hydroxyl cholesterol. | |||||||||
![]() | cryo-EM structure of Scap/Insig in the present of 25HC | |||||||||
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![]() | Scap / Insig / cholesterol / sterol sensing / 25-hydroxycholesterol / SREBP / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 / 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 / negative regulation of cholesterol biosynthetic process / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Yan R / Cao P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A structure of human Scap bound to Insig-2 suggests how their interaction is regulated by sterols. Authors: Renhong Yan / Pingping Cao / Wenqi Song / Hongwu Qian / Ximing Du / Hudson W Coates / Xin Zhao / Yaning Li / Shuai Gao / Xin Gong / Ximing Liu / Jianhua Sui / Jianlin Lei / Hongyuan Yang / ...Authors: Renhong Yan / Pingping Cao / Wenqi Song / Hongwu Qian / Ximing Du / Hudson W Coates / Xin Zhao / Yaning Li / Shuai Gao / Xin Gong / Ximing Liu / Jianhua Sui / Jianlin Lei / Hongyuan Yang / Andrew J Brown / Qiang Zhou / Chuangye Yan / Nieng Yan / ![]() ![]() ![]() 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 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 97.1 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() | 28.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m49MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryo-EM structure of Scap/Insig in the present of 25HC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_30074_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Scap and Insig complex
Entire | Name: Scap and Insig complex |
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Components |
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-Supramolecule #1: Scap and Insig complex
Supramolecule | Name: Scap and Insig complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Insulin-induced gene 2 protein
Macromolecule | Name: Insulin-induced gene 2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.74966 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAEGETESPG PKKSGPYISS VTSQSVNLMI RGVVLFFIGV FLALVLNLLQ IQRNVTLFPP DVIASIFSSA WWVPPCCGTA SAVIGLLYP SIDRHLGEPH KFKREWSSVM RCVAVFVGIN HASAKVDFDN NIQLSLTLAA LSIGLWWTFD RSRSGFGLGV G IAFLATVV ...String: MAEGETESPG PKKSGPYISS VTSQSVNLMI RGVVLFFIGV FLALVLNLLQ IQRNVTLFPP DVIASIFSSA WWVPPCCGTA SAVIGLLYP SIDRHLGEPH KFKREWSSVM RCVAVFVGIN HASAKVDFDN NIQLSLTLAA LSIGLWWTFD RSRSGFGLGV G IAFLATVV TQLLVYNGVY QYTSPDFLYV RSWLPCIFFA GGITMGNIGR QLAMYESKVI AEKSHQE UniProtKB: Insulin-induced gene 2 protein |
-Macromolecule #2: Sterol regulatory element-binding protein cleavage-activating pro...
Macromolecule | Name: Sterol regulatory element-binding protein cleavage-activating protein,Sterol regulatory element-binding protein cleavage-activating protein type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 63.295406 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MTLTERLREK ISRAFYNHGL LCASYPIPII LFTGFCILAC CYPLLKLPLP GTVPGKYSGV SLYTRKRMVS YTITLVFQHY HAKFLGSLR ARLMLLHPSP NCSLRAESLV HVHFKEEIGV AELIPLVTTY IILFAYIYFS TRKIDMVKSK WGLALAAVVT V LSSLLMSV ...String: MTLTERLREK ISRAFYNHGL LCASYPIPII LFTGFCILAC CYPLLKLPLP GTVPGKYSGV SLYTRKRMVS YTITLVFQHY HAKFLGSLR ARLMLLHPSP NCSLRAESLV HVHFKEEIGV AELIPLVTTY IILFAYIYFS TRKIDMVKSK WGLALAAVVT V LSSLLMSV GLCTLFGLTP TLNGGEIFPY LVVVIGLENV LVLTKSVVST PVDLEVKLRI AQGLSSESWS IMKNMATELG II LIGYFTL VPAIQEFCLF AVVGLVSDFF LQMLFFTTVL SIDIRRMELA DLNKRLPPEA CLPSAKPVGQ PTRYERQLAV RPS TPHTIT LQPSSFRNLR LPKRLRVVYF LARTRLAQRL IMAGTVVWIG ILVYTDPAGL RNYLAAQVTE QSPLGEGALA PMPV PSGML PPSHPDPAFS IFPPDAPKLP ENQTSPGESP ERGGPAEVVH DSPVPEVTWG PEDEELWRKL SFRHWPTLFS YYNIT LAKR YISLLPVIPV TLRLNPREAL EGRHPQDGRS AWPPPGPIPA GHWEAGPKGP GGVQAHGDVT LYKVAALGLA TGIVLV LLL LCLYRVLCP UniProtKB: Sterol regulatory element-binding protein cleavage-activating protein, Sterol regulatory element-binding protein cleavage-activating protein |
-Macromolecule #3: 25-HYDROXYCHOLESTEROL
Macromolecule | Name: 25-HYDROXYCHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: HC3 |
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Molecular weight | Theoretical: 402.653 Da |
Chemical component information | ![]() ChemComp-HC3: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153168 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |