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Yorodumi- EMDB-40799: Cryo-EM consensus map of a double loaded human UBA7-UBE2L6-ISG15 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40799 | |||||||||
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Title | Cryo-EM consensus map of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ubiquitin / SIGNALING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Afsar M / Jia L / Ruben EA / Olsen SK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Authors: Mohammad Afsar / GuanQun Liu / Lijia Jia / Eliza A Ruben / Digant Nayak / Zuberwasim Sayyad / Priscila Dos Santos Bury / Kristin E Cano / Anindita Nayak / Xiang Ru Zhao / Ankita Shukla / ...Authors: Mohammad Afsar / GuanQun Liu / Lijia Jia / Eliza A Ruben / Digant Nayak / Zuberwasim Sayyad / Priscila Dos Santos Bury / Kristin E Cano / Anindita Nayak / Xiang Ru Zhao / Ankita Shukla / Patrick Sung / Elizabeth V Wasmuth / Michaela U Gack / Shaun K Olsen / Abstract: ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin- ...ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40799.map.gz | 85.9 MB | EMDB map data format | |
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Header (meta data) | emd-40799-v30.xml emd-40799.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_40799.png | 20.6 KB | ||
Masks | emd_40799_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-40799.cif.gz | 4 KB | ||
Others | emd_40799_half_map_1.map.gz emd_40799_half_map_2.map.gz | 163.4 MB 163.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40799 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40799 | HTTPS FTP |
-Validation report
Summary document | emd_40799_validation.pdf.gz | 814 KB | Display | EMDB validaton report |
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Full document | emd_40799_full_validation.pdf.gz | 813.5 KB | Display | |
Data in XML | emd_40799_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_40799_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40799 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40799 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40799.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8332 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40799_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40799_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40799_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex
Entire | Name: Double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex |
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Components |
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-Supramolecule #1: Double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex
Supramolecule | Name: Double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.888 µm / Nominal defocus min: 0.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225140 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |