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Yorodumi- EMDB-19567: Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G7... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19567 | ||||||||||||||||||
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Title | Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub | ||||||||||||||||||
Map data | Cryo-EM structure of the (NEDD8)-CRL2VHL-MZ1-Brd4BD2 ternary complex primed for catalysis with UBE2R1-Ub. | ||||||||||||||||||
Sample |
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Keywords | E3 ligase / Cullin / PROTAC / BET bromodomain / LIGASE | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of inclusion body assembly / regulation of cellular response to hypoxia / (E3-independent) E2 ubiquitin-conjugating enzyme / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / target-directed miRNA degradation / response to growth factor ...positive regulation of inclusion body assembly / regulation of cellular response to hypoxia / (E3-independent) E2 ubiquitin-conjugating enzyme / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / target-directed miRNA degradation / response to growth factor / elongin complex / VCB complex / protein neddylation / negative regulation of cAMP-mediated signaling / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / ubiquitin conjugating enzyme activity / TGF-beta receptor signaling activates SMADs / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / DNA replication initiation / P-TEFb complex binding / anatomical structure morphogenesis / protein K48-linked ubiquitination / negative regulation by host of viral transcription / Tat-mediated elongation of the HIV-1 transcript / cellular response to interferon-beta / Formation of HIV-1 elongation complex containing HIV-1 Tat / positive regulation of T-helper 17 cell lineage commitment / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of TORC1 signaling / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / RNA Polymerase II Pre-transcription Events / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of G2/M transition of mitotic cell cycle / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / histone reader activity / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / RNA polymerase II CTD heptapeptide repeat kinase activity / Downregulation of TGF-beta receptor signaling / intrinsic apoptotic signaling pathway / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
Authors | Ciulli A / Crowe C / Nakasone MA | ||||||||||||||||||
Funding support | European Union, United Kingdom, Switzerland, 5 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Mechanism of degrader-targeted protein ubiquitinability Authors: Crowe C / Nakasone MA / Chandler S / Tatham MH / Makukhin N / Hay RT / Ciulli A | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19567.map.gz | 398.5 MB | EMDB map data format | |
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Header (meta data) | emd-19567-v30.xml emd-19567.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19567_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_19567.png | 110.9 KB | ||
Filedesc metadata | emd-19567.cif.gz | 4.1 KB | ||
Others | emd_19567_half_map_1.map.gz emd_19567_half_map_2.map.gz | 391.3 MB 391.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19567 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19567 | HTTPS FTP |
-Related structure data
Related structure data | 8rx0M C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19567.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of the (NEDD8)-CRL2VHL-MZ1-Brd4BD2 ternary complex primed for catalysis with UBE2R1-Ub. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_19567_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19567_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G7...
Entire | Name: Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub |
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Components |
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-Supramolecule #1: Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G7...
Supramolecule | Name: Closed crosslinked structure of (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 190 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |