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Yorodumi- EMDB-30386: Negative-stain EM 3D reconstruction of UGGT with the Fab of monoc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30386 | |||||||||
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Title | Negative-stain EM 3D reconstruction of UGGT with the Fab of monoclonal antibody directed against the Trx4 domain. | |||||||||
Map data | Negative-stain EM 3D reconstruction of UGGT with the Fab of monoclonal antibody | |||||||||
Sample |
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Biological species | Thermomyces dupontii (fungus) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.9 Å | |||||||||
Authors | Satoh T / Song C / Murata K / Kato K | |||||||||
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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30386.map.gz | 27.8 MB | EMDB map data format | |
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Header (meta data) | emd-30386-v30.xml emd-30386.xml | 7.6 KB 7.6 KB | Display Display | EMDB header |
Images | emd_30386.png | 35.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30386 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30386 | HTTPS FTP |
-Validation report
Summary document | emd_30386_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_30386_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_30386_validation.xml.gz | 496 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30386 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30386 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30386.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative-stain EM 3D reconstruction of UGGT with the Fab of monoclonal antibody | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.98 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 : UGGT with the Fab of monoclonal antibody directed against the Trx...
Entire | Name: UGGT with the Fab of monoclonal antibody directed against the Trx4 domain. |
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Components |
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-Supramolecule #1: UGGT with the Fab of monoclonal antibody directed against the Trx...
Supramolecule | Name: UGGT with the Fab of monoclonal antibody directed against the Trx4 domain. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermomyces dupontii (fungus) |
Recombinant expression | Organism: Tobacco etch virus |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.7 |
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Staining | Type: NEGATIVE / Material: uranyl acetate |
-Electron microscopy
Microscope | JEOL 2200FS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2251 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |