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Yorodumi- EMDB-31303: Cryo-EM structure of Scap/Insig complex in the present of digitonin. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31303 | |||||||||
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Title | Cryo-EM structure of Scap/Insig complex in the present of digitonin. | |||||||||
Map data | cryo-EM structure of Insig-2/Scap complex in the presence of digitonin | |||||||||
Sample |
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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 / 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 | Homo sapiens (human) | |||||||||
Method | 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, 1 items
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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 |
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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_31303.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-31303-v30.xml emd-31303.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_31303.png | 154.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31303 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31303 | HTTPS FTP |
-Validation report
Summary document | emd_31303_validation.pdf.gz | 440.4 KB | Display | EMDB validaton report |
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Full document | emd_31303_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | emd_31303_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_31303_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31303 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31303 | HTTPS FTP |
-Related structure data
Related structure data | 7etwMC 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_31303.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 Insig-2/Scap complex in the presence of digitonin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-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) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S |
-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 |
-Macromolecule #2: Sterol regulatory element-binding protein cleavage-activating protein
Macromolecule | Name: 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: 81.863531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTLTERLREK ISRAFYNHGL LCASYPIPII LFTGFCILAC CYPLLKLPLP GTGPVEFTTP VKDYSPPPVD SDRKQGEPTE QPEWYVGAP VAYVQQIFVK SSVFPWHKNL LAVDVFRSPL SRAFQLVEEI RNHVLRDSSG IRSLEELCLQ VTDLLPGLRK L RNLLPEHG ...String: MTLTERLREK ISRAFYNHGL LCASYPIPII LFTGFCILAC CYPLLKLPLP GTGPVEFTTP VKDYSPPPVD SDRKQGEPTE QPEWYVGAP VAYVQQIFVK SSVFPWHKNL LAVDVFRSPL SRAFQLVEEI RNHVLRDSSG IRSLEELCLQ VTDLLPGLRK L RNLLPEHG CLLLSPGNFW QNDWERFHAD PDIIGTIHQH EPKTLQTSAT LKDLLFGVPG KYSGVSLYTR KRMVSYTITL VF QHYHAKF LGSLRARLML LHPSPNCSLR AESLVHVHFK EEIGVAELIP LVTTYIILFA YIYFSTRKID MVKSKWGLAL AAV VTVLSS LLMSVGLCTL FGLTPTLNGG EIFPYLVVVI GLENVLVLTK SVVSTPVDLE VKLRIAQGLS SESWSIMKNM ATEL GIILI GYFTLVPAIQ EFCLFAVVGL VSDFFLQMLF FTTVLSIDIR RMELADLNKR LPPEACLPSA KPVGQPTRYE RQLAV RPST PHTITLQPSS FRNLRLPKRL RVVYFLARTR LAQRLIMAGT VVWIGILVYT DPAGLRNYLA AQVTEQSPLG EGALAP MPV PSGMLPPSHP DPAFSIFPPD APKLPENQTS PGESPERGGP AEVVHDSPVP EVTWGPEDEE LWRKLSFRHW PTLFSYY NI TLAKRYISLL PVIPVTLRLN PREALEGRHP QDGRSAWPPP GPIPAGHWEA GPKGPGGVQA HGDVTLYKVA ALGLATGI V LVLLLLCLYR VLCP |
-Macromolecule #4: Digitonin
Macromolecule | Name: Digitonin / type: ligand / ID: 4 / Number of copies: 4 / Formula: AJP |
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Molecular weight | Theoretical: 1.229312 KDa |
Chemical component information | ChemComp-AJP: |
-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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 252929 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |