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Yorodumi- EMDB-18767: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18767 | |||||||||
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Title | K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB~acceptor UB-BRD4 | |||||||||
Map data | DeepEMhancer sharpened map | |||||||||
Sample |
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Keywords | CUL2 / VHL / ELOBC / BRD4 / MZ1 / PROTAC / Ubiquitin / Ubiquitin Ligase / Ubiquitin chain formation / Poliubiquitylation / LIGASE / NEDD8 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Liwocha J / Prabu JR / Kleiger G / Schulman BA | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Authors: Joanna Liwocha / Jerry Li / Nicholas Purser / Chutima Rattanasopa / Samuel Maiwald / David T Krist / Daniel C Scott / Barbara Steigenberger / J Rajan Prabu / Brenda A Schulman / Gary Kleiger / Abstract: E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked ...E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18767.map.gz | 16.1 MB | EMDB map data format | |
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Header (meta data) | emd-18767-v30.xml emd-18767.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18767_fsc.xml | 6.1 KB | Display | FSC data file |
Images | emd_18767.png | 58.3 KB | ||
Masks | emd_18767_msk_1.map | 18.1 MB | Mask map | |
Filedesc metadata | emd-18767.cif.gz | 4.4 KB | ||
Others | emd_18767_additional_1.map.gz emd_18767_half_map_1.map.gz emd_18767_half_map_2.map.gz | 1.7 MB 13.8 MB 13.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18767 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18767 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18767.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | DeepEMhancer sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.925 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18767_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Postprocessed map
File | emd_18767_additional_1.map | ||||||||||||
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Annotation | Postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18767_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18767_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : K48-linked ubiquitin chain formation with a cullin-RING E3 ligase...
Entire | Name: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB~acceptor UB-BRD4 |
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Components |
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-Supramolecule #1: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase...
Supramolecule | Name: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB~acceptor UB-BRD4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Molecular weight | Theoretical: 190 KDa |
-Supramolecule #2: RING E3 ligase (RBX1) and Cullin-2 (CUL2)
Supramolecule | Name: RING E3 ligase (RBX1) and Cullin-2 (CUL2) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: NEDD8, ELOB, ELOC, VHL-MZ1, UBE2R2-donor UB-acceptor UB-BRD4 and ...
Supramolecule | Name: NEDD8, ELOB, ELOC, VHL-MZ1, UBE2R2-donor UB-acceptor UB-BRD4 and K48-linked ubiquitin chain type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2, #5-#6 |
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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-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |