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Yorodumi- EMDB-9537: Complex structure of the fission yeast SREBP-SCAP binding domains -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9537 | |||||||||
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Title | Complex structure of the fission yeast SREBP-SCAP binding domains | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of ergosterol biosynthetic process / regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / negative regulation of cellular response to hypoxia / sterol binding / SREBP signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / steroid metabolic process / cellular response to hypoxia ...positive regulation of ergosterol biosynthetic process / regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / negative regulation of cellular response to hypoxia / sterol binding / SREBP signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / steroid metabolic process / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / endoplasmic reticulum membrane / chromatin / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Gong X / Qian HW / Wu JP / Yan N | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2016 Title: Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization. Authors: Xin Gong / Hongwu Qian / Wei Shao / Jingxian Li / Jianping Wu / Jun-Jie Liu / Wenqi Li / Hong-Wei Wang / Peter Espenshade / Nieng Yan / Abstract: Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. ...Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation. | |||||||||
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_9537.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-9537-v30.xml emd-9537.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_9537.png | 62.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9537 | HTTPS FTP |
-Validation report
Summary document | emd_9537_validation.pdf.gz | 428.1 KB | Display | EMDB validaton report |
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Full document | emd_9537_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | emd_9537_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_9537_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9537 | HTTPS FTP |
-Related structure data
Related structure data | 5grsMC 5gpdC 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_9537.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.32 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 : Complex structure of the fission yeast SREBP-SCAP binding domains
Entire | Name: Complex structure of the fission yeast SREBP-SCAP binding domains |
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Components |
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-Supramolecule #1: Complex structure of the fission yeast SREBP-SCAP binding domains
Supramolecule | Name: Complex structure of the fission yeast SREBP-SCAP binding domains type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET15b, pETDuet-1 |
-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 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 44.95675 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGWSDHDELS TDTTLHEEKF RIEPVPVHHQ LDILKIAVSE NYKTFASVGL DRCLVVWDLR QWCTKLVLSK EQMPRTLKAI ALDPQGNYV SLFSKDTLFI LNVESPSLML QHSYHCKPNS KLNVFWMPGT HKDDEWKNFE LVVVESSGEI QVFSLTIEIE G ADIALVEK ...String: MGWSDHDELS TDTTLHEEKF RIEPVPVHHQ LDILKIAVSE NYKTFASVGL DRCLVVWDLR QWCTKLVLSK EQMPRTLKAI ALDPQGNYV SLFSKDTLFI LNVESPSLML QHSYHCKPNS KLNVFWMPGT HKDDEWKNFE LVVVESSGEI QVFSLTIEIE G ADIALVEK FQLSSPIIKS ISIVSPTANR IACLTESGEV TVYSKKGPVW SPKILSQNKN YLTETKKDIY GIAMADILFL AR DSGVDMI DLKNDELLHS FTLPPIKVNT FSVGVSNSRF VNGQFRVSSI SFCFTHAVTE KVLYYYYGNE SNESYIILNK WDQ QPNLVD VHDPDNSLAS LTFDELQENI HEVEDASESV MSSDGLYIFG MRRKSSSGIS PTADEKNEDN GFTLRNRKLR |
-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: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 11.868574 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AHMNTHSGGE TQVWEVWMYS QSEKKHRSKS LKMYNSLIIA DPGPSLAVSD RCVAIVLGNY VALVGYGSEI FRDFYQIRNS DEMDRILRR KRKNLQRKRS GTIG |
-Macromolecule #3: Sterol regulatory element-binding protein 1
Macromolecule | Name: Sterol regulatory element-binding protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 30.318842 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AHMQHSKSSV HAELRELPES TANLIENSHA DDVFSPNMVE RLWVLAKSTR DSAQMSDSII SSLSDVLVLS PLEVLASWYA ADLLDALLM ESLSRKVEIS EIEEIISLCP KNSSIIRHAL LAKLVLFPEN TADSLNEVLA AYKNTLDLCS QDKRKQSSVL K INLSKLFT ...String: AHMQHSKSSV HAELRELPES TANLIENSHA DDVFSPNMVE RLWVLAKSTR DSAQMSDSII SSLSDVLVLS PLEVLASWYA ADLLDALLM ESLSRKVEIS EIEEIISLCP KNSSIIRHAL LAKLVLFPEN TADSLNEVLA AYKNTLDLCS QDKRKQSSVL K INLSKLFT LHSCLSLALQ RLGYGDVSKR MYQEIFVPDS DADITPLSFI ISWTALNTFA PICTSPKEND VVEKMAMYVR TA IGTLKIQ DLKLSRKLIN SCIDIGSRLQ EDLGY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 20 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157243 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |