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Yorodumi- EMDB-30074: cryo-EM structure of Scap/Insig complex in the present of 25-hydr... -
+Open data
-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. | |||||||||
Map data | cryo-EM structure of Scap/Insig in the present of 25HC | |||||||||
Sample |
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Keywords | Scap / Insig / cholesterol / sterol sensing / 25-hydroxycholesterol / SREBP / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / negative regulation of steroid biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / COPII-coated vesicle cargo loading ...SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / negative regulation of steroid biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / 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) / negative regulation of cholesterol biosynthetic process / oxysterol binding / triglyceride metabolic process / middle ear morphogenesis / inner ear morphogenesis / roof of mouth development / cholesterol biosynthetic process / cholesterol metabolic process / protein sequestering activity / response to insulin / ER to Golgi transport vesicle membrane / cellular response to insulin stimulus / unfolded protein binding / response to hypoxia / immune response / Golgi membrane / protein-containing complex binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Yan R / Cao P | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30074.map.gz | 28.7 MB | EMDB map data format | |
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Header (meta data) | emd-30074-v30.xml emd-30074.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
Images | emd_30074.png | 97.1 KB | ||
Filedesc metadata | emd-30074.cif.gz | 5.8 KB | ||
Others | emd_30074_additional_1.map.gz | 28.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30074 | HTTPS FTP |
-Related structure data
Related structure data | 6m49MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30074.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
-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: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 24.74966 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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: Homo sapiens (human) |
Molecular weight | Theoretical: 63.295406 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153168 |