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Yorodumi- PDB-5y7f: Crystal structure of catalytic domain of UGGT (UDP-bound form) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y7f | ||||||||||||
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Title | Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii | ||||||||||||
Components | UGGT | ||||||||||||
Keywords | TRANSFERASE / ENDOPLASMIC RETICULUM / QUALITY CONTROL / GLUCOSYLTRANSFERASE / FOLDING SENSOR | ||||||||||||
Function / homology | Function and homology information UDP-glucose:glycoprotein glucosyltransferase activity / sporulation / anatomical structure development / protein glycosylation Similarity search - Function | ||||||||||||
Biological species | Thermomyces dupontii (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Satoh, T. / Song, C. / Zhu, T. / Toshimori, T. / Murata, K. / Hayashi, Y. / Kamikubo, H. / Uchihashi, T. / Kato, K. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT. Authors: Tadashi Satoh / Chihong Song / Tong Zhu / Takayasu Toshimori / Kazuyoshi Murata / Yugo Hayashi / Hironari Kamikubo / Takayuki Uchihashi / Koichi Kato / Abstract: In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates ...In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y7f.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y7f.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y7f_validation.pdf.gz | 766.6 KB | Display | wwPDB validaton report |
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Full document | 5y7f_full_validation.pdf.gz | 767.9 KB | Display | |
Data in XML | 5y7f_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5y7f_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y7f ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y7f | HTTPS FTP |
-Related structure data
Related structure data | 5h18SC 5y7oC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35097.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomyces dupontii (fungus) / Plasmid: PCOLD-I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCJ6*PLUS |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-TRS / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Crystallization buffer 24% PEG 3350, 100 MM TRIS-HCL (PH 9.0), Soaking buffer 24% PEG 3350, 100 MM TRIS-HCL (PH 9.0), 2 mM CaCl2, 10 mM UDP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 62275 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.796 / Num. unique obs: 9467 / CC1/2: 0.75 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H18 Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.155 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.615 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→20 Å
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Refine LS restraints |
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