+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23407 | ||||||||||||||||||||||||||||||||||||
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Title | Map of full mutant cScap/Fab complex | ||||||||||||||||||||||||||||||||||||
Map data | Map of Scap(D435VB)/Insig-1/4G10 complex complex. Low pass filtered by local resolution | ||||||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / regulation of fatty acid biosynthetic process / positive regulation of cholesterol biosynthetic process / cholesterol metabolic process / response to insulin ...Regulation of cholesterol biosynthesis by SREBP (SREBF) / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / cellular lipid metabolic process / sterol binding / regulation of fatty acid biosynthetic process / positive regulation of cholesterol biosynthetic process / cholesterol metabolic process / response to insulin / ER to Golgi transport vesicle membrane / membrane => GO:0016020 / response to hypoxia / immune response / Golgi membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Gallus gallus (chicken) / Mus musculus (house mouse) / Mouse (mice) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||||||||||||||||||||||||||
Authors | Kober DL / Radhakrishnan A / Goldstein JL / Brown MS / Clark LD / Bai X-C / Rosenbaum DM | ||||||||||||||||||||||||||||||||||||
Funding support | United States, France, 11 items
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Citation | Journal: Cell / Year: 2021 Title: Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing. Authors: Daniel L Kober / Arun Radhakrishnan / Joseph L Goldstein / Michael S Brown / Lindsay D Clark / Xiao-Chen Bai / Daniel M Rosenbaum / Abstract: The cholesterol-sensing protein Scap induces cholesterol synthesis by transporting membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) from the endoplasmic ...The cholesterol-sensing protein Scap induces cholesterol synthesis by transporting membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) from the endoplasmic reticulum (ER) to the Golgi apparatus for proteolytic activation. Transport requires interaction between Scap's two ER luminal loops (L1 and L7), which flank an intramembrane sterol-sensing domain (SSD). Cholesterol inhibits Scap transport by binding to L1, which triggers Scap's binding to Insig, an ER retention protein. Here we used cryoelectron microscopy (cryo-EM) to elucidate two structures of full-length chicken Scap: (1) a wild-type free of Insigs and (2) mutant Scap bound to chicken Insig without cholesterol. Strikingly, L1 and L7 intertwine tightly to form a globular domain that acts as a luminal platform connecting the SSD to the rest of Scap. In the presence of Insig, this platform undergoes a large rotation accompanied by rearrangement of Scap's transmembrane helices. We postulate that this conformational change halts Scap transport of SREBPs and inhibits cholesterol synthesis. | ||||||||||||||||||||||||||||||||||||
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_23407.map.gz | 47.1 MB | EMDB map data format | |
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Header (meta data) | emd-23407-v30.xml emd-23407.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23407_fsc.xml | 9.7 KB | Display | FSC data file |
Images | emd_23407.png | 17.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23407 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23407 | HTTPS FTP |
-Related 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_23407.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of Scap(D435VB)/Insig-1/4G10 complex complex. Low pass filtered by local resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 : Ternary complex of Scap with Fab fragment
Entire | Name: Ternary complex of Scap with Fab fragment |
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Components |
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-Supramolecule #1: Ternary complex of Scap with Fab fragment
Supramolecule | Name: Ternary complex of Scap with Fab fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Fab fragment generated by proteolytic cleavage of IgG antibody |
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Molecular weight | Theoretical: 50 KDa |
-Supramolecule #2: Scap
Supramolecule | Name: Scap / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: 4G10 Fab
Supramolecule | Name: 4G10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 Details: Fab fragment generated by proteolytic cleavage of IgG antibody |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Sterol regulatory element-binding protein cleavage-activating protein
Macromolecule | Name: Sterol regulatory element-binding protein cleavage-activating protein type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PAMTLTEKLR ERISRAFYNH GLLCASYPIP IILFTGLCIL ACCYPLLKLP LPGTGPVEFS TPVKDYFPPS PDVVSQQGDL SERPDWYVGA PVAYIQQIFV KATVSPWQKN FLAVDVFRSP LSRVFQLVEE IRNHALRDSS GVKSLEEVCL QVTDLLPGLK KLRNLLPEHG ...String: PAMTLTEKLR ERISRAFYNH GLLCASYPIP IILFTGLCIL ACCYPLLKLP LPGTGPVEFS TPVKDYFPPS PDVVSQQGDL SERPDWYVGA PVAYIQQIFV KATVSPWQKN FLAVDVFRSP LSRVFQLVEE IRNHALRDSS GVKSLEEVCL QVTDLLPGLK KLRNLLPEHG CLLLSPGNFW QNDRERFNAD PDIIKTIHQH EPKALQTSAT LKDLLFGLPG KYSGVNLYNR KRVVSYTVTL GLQRYDSRFL SSLRSRLKLL HPSPNCTLRE DSIVHVHFKE EIGIAELIPL VTTYIILFAY IYFSTRKIDM VKSKWGLALA AVVTVLSSLL MSVGLCTLFG LTPTLNGGSV PVSFREIFPY LVVVIGLENV LVLTKSVVST PVDLEVKLRI AQGLSNESWS IMKNMATELG IILIGYFTLV PAIQEFCLFA VVGLVSVFFL QMLFFTTVLS IDIRRMELAD LNKRLPAEAC LPPAKPASRS QRYERQPAVR PATPHTITLQ PSSFRNLRLP KRLRVIYFFA RTRLAQRLIM AGTVIWIGIL VYTDPAGLRT YLTSQVTEQS PLGEAGLPPM PVPGGVLPAG DPKIDLSVFP SDPIQLSENQ TQQREQQAGL EPLGRLETNQ HSWAQGPEGR GNGQTELGTE AEVTWGAEDE EIWRKLSFRH WPSLFSYYNI TLAKRYISIL PAIPVTLYLN PQEALEVRHP QEANRYHPFL SSSGGKLNAE AQPDQTSSRL QGHRDVTLYK VAALGLASGI LLVLLLFCLY RLLCPKNYGQ NGLSHSRRRR GDLPCDDYGY SPPETEIVPL VLRGHLMDIE CLASDGMLLV SCCLVGQIRV WDAQTGDCLT VIPKPRLRRD SSGIFDYQES WDHSPDGKTG LDDSFESSHQ LKRMLSPPQP PLFCDQPDLT SLIDTNFSEQ VKVAESEPRL RAVGGRQKEA GYDFSSLVGK VYEEHSTSNC MNFGGLSAPH GQAGFCVGGS TARSLGCGSE EGGCGGRRRS LGDESLSGFD KSSPLPSWGG DFESSVWSLD LQGNLIVAGR SNGKLEVWDA IEGTLRSSND ESQSGITALV FLNNRIVAAR LNGSLDFFSL ETHTSLNHLQ FRGAPSRSSI PSSPLFSSSD VIVCQLTHTV SCAHQKPITA LKAAAGRLVT GSQDHTLRVF RLEDSCCLFT LQGHSGAITA VYIDQTMVLA SGGQDGAICL WDVLTGSKVS HMYAHRGDVT SLTCTTSCVI SSGLDDVISI WDRSSGIKLY SIQQEMGCGS SLGVISDNLL VTGGQGCVSF WDIGYGDLLQ TVYLGKSNES QPARQILVLE NAAIVCNFGS ELSLVYVPSV LEKLDDYKDD DDKGSDYKDD DDKGSDYKDD DDK |
-Macromolecule #2: Insig-1
Macromolecule | Name: Insig-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTGPKADAMQ SPSPSAGRAE REASGGSATT WRQHLVQRSV VLFVVGAFMA LVLNLLQIQR NVTLFPDEVI ATLFSSAWWV PPCCGTAAAV VGLLYPCIDS HLGEPHKFKR EWASVMRCIA VFVGINHASA KLDFANNVQL SLTLAALSLG LWWTFDRSRS GLGLGITIAF ...String: MTGPKADAMQ SPSPSAGRAE REASGGSATT WRQHLVQRSV VLFVVGAFMA LVLNLLQIQR NVTLFPDEVI ATLFSSAWWV PPCCGTAAAV VGLLYPCIDS HLGEPHKFKR EWASVMRCIA VFVGINHASA KLDFANNVQL SLTLAALSLG LWWTFDRSRS GLGLGITIAF VATLITQFLV YNGVYQYTSP DFLYIRSWLP CIFFSGGVTV GNIGRQLAMG IPEKPHNDSR ENLYFQGGSG ATNFSLLKQA GDVEENPG |
-Macromolecule #3: 4G10 Fab light chain
Macromolecule | Name: 4G10 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mouse (mice) |
Sequence | String: DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQQ TNTLPWTFGG GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD ...String: DIQMTQTTSS LSASLGDRVT ISCRASQDIR NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQQ TNTLPWTFGG GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC |
-Macromolecule #4: 4G10 Fab heavy chain
Macromolecule | Name: 4G10 Fab heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mouse (mice) |
Sequence | String: TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLSS LTSEDTAVYY CTRYNDYDAF YFDYWGQGTT LTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA ...String: TGVHSEVQLQ QSGAELVRPG ASVKLSCTAS GFKIKDDYIH WVKQRPEQGL EWIGRIDPAN GHTRYAPKFQ DKATITADTS SNTAYLQLSS LTSEDTAVYY CTRYNDYDAF YFDYWGQGTT LTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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 BIOQUANTUM (6k x 4k) / Average electron dose: 1.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |