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Yorodumi- PDB-5grs: Complex structure of the fission yeast SREBP-SCAP binding domains -
+Open data
-Basic information
Entry | Database: PDB / ID: 5grs | |||||||||
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Title | Complex structure of the fission yeast SREBP-SCAP binding domains | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / protein complex | |||||||||
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 / SREBP signaling pathway / sterol binding / negative regulation of cellular response to hypoxia / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / cellular response to hypoxia ...positive regulation of ergosterol biosynthetic process / regulation of ergosterol biosynthetic process / SREBP-SCAP complex / regulation of cholesterol biosynthetic process / SREBP signaling pathway / sterol binding / negative regulation of cellular response to hypoxia / steroid metabolic process / cytoplasmic side of endoplasmic reticulum membrane / 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 / chromatin / endoplasmic reticulum membrane / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Gong, X. / Qian, H.W. / Wu, J.P. / Yan, N. | |||||||||
Funding support | China, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5grs.cif.gz | 616.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5grs.ent.gz | 521.4 KB | Display | PDB format |
PDBx/mmJSON format | 5grs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/5grs ftp://data.pdbj.org/pub/pdb/validation_reports/gr/5grs | HTTPS FTP |
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-Related structure data
Related structure data | 9537MC 5gpdC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44956.750 Da / Num. of mol.: 4 / Fragment: UNP residues 567-961 / Mutation: C671S, C873S, C901S, C920S, C941S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: scp1, SPBC3B9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: O43043 #2: Protein | Mass: 11868.574 Da / Num. of mol.: 4 / Fragment: UNP residues 986-1085 / Mutation: C1010S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: scp1, SPBC3B9.15c / Production host: Escherichia coli (E. coli) / References: UniProt: O43043 #3: Protein | Mass: 30318.842 Da / Num. of mol.: 4 / Fragment: UNP residues 628-896 / Mutation: C644S, C672S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: sre1, SPBC19C2.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UUD1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex structure of the fission yeast SREBP-SCAP binding domains Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Schizosaccharomyces pombe 972h- (yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pET15b, pETDuet-1 |
Buffer solution | pH: 8 |
Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157243 / Symmetry type: POINT |