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Yorodumi- EMDB-62081: Structure of substrate-engaged human 26S proteasome RP-CP subcomp... -
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Open data
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Basic information
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| Title | Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.3 | |||||||||
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Keywords | Proteasome / AAA-ATPase / Deubiquitinase / HYDROLASE | |||||||||
| Function / homology | Function and homology informationpositive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / proteasome regulatory particle ...positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / proteasome regulatory particle / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / cytosolic proteasome complex / CD8-positive, alpha-beta T cell homeostasis / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / protein K63-linked deubiquitination / cellular response to type I interferon / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / T-helper 17 cell differentiation / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Cross-presentation of soluble exogenous antigens (endosomes) / transcription factor binding / Somitogenesis / flagellated sperm motility / K63-linked deubiquitinase activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Formation of the ternary complex, and subsequently, the 43S complex / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Impaired BRCA2 binding to RAD51 / myofibril / SARS-CoV-1 modulates host translation machinery / proteasomal ubiquitin-independent protein catabolic process / Peptide chain elongation / general transcription initiation factor binding / Selenocysteine synthesis / Formation of a pool of free 40S subunits / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / protein deubiquitination / Viral mRNA Translation / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / endopeptidase activator activity / GTP hydrolysis and joining of the 60S ribosomal subunit / threonine-type endopeptidase activity / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome core complex, alpha-subunit complex / proteasome assembly / mRNA export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / immune system process / regulation of G1/S transition of mitotic cell cycle / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / enzyme regulator activity / regulation of macroautophagy / positive regulation of interleukin-2 production / ciliary tip / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / response to type II interferon / Maturation of protein E / inclusion body / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Wu Z / Chen E / Mao Y | |||||||||
| Funding support | China, 1 items
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Citation | Journal: To be publishedTitle: Hidden dynamics of ubiquitin-mediated proteasome autoregulation during protein degradation Authors: Wu Z / Chen E / Zou S / Hou Y / Zhang S / Wang W / Dong Y / Mao Y | |||||||||
| History |
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_62081.map.gz | 742.4 MB | EMDB map data format | |
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| Header (meta data) | emd-62081-v30.xml emd-62081.xml | 61.5 KB 61.5 KB | Display Display | EMDB header |
| Images | emd_62081.png | 64.1 KB | ||
| Filedesc metadata | emd-62081.cif.gz | 14.8 KB | ||
| Others | emd_62081_half_map_1.map.gz emd_62081_half_map_2.map.gz | 702.4 MB 703.2 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-62081 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-62081 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9k55MC ![]() 9k4jC ![]() 9k4kC ![]() 9k4lC ![]() 9k4mC ![]() 9k4oC ![]() 9k4pC ![]() 9k4rC ![]() 9k4sC ![]() 9k4tC ![]() 9k4uC ![]() 9k4vC ![]() 9k4wC ![]() 9k4xC ![]() 9k4yC ![]() 9k4zC ![]() 9k50C ![]() 9k51C ![]() 9k53C ![]() 9k54C ![]() 9k56C ![]() 9k57C ![]() 9k58C ![]() 9k59C ![]() 9k5aC ![]() 9k5bC ![]() 9k5cC ![]() 9k5dC ![]() 9k5eC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_62081.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.685 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #1
| File | emd_62081_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_62081_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 26S proteasome
+Supramolecule #1: 26S proteasome
+Macromolecule #1: 26S proteasome regulatory subunit 7
+Macromolecule #2: 26S proteasome regulatory subunit 4
+Macromolecule #3: 26S proteasome regulatory subunit 8
+Macromolecule #4: 26S proteasome regulatory subunit 6B
+Macromolecule #5: Proteasome 26S subunit, ATPase 6
+Macromolecule #6: 26S proteasome regulatory subunit 6A
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit alpha type-2
+Macromolecule #9: Proteasome subunit alpha type-4
+Macromolecule #10: Proteasome subunit alpha type-7
+Macromolecule #11: Proteasome subunit alpha type-5
+Macromolecule #12: Proteasome subunit alpha type-1
+Macromolecule #13: Proteasome subunit alpha type-3
+Macromolecule #14: Proteasome subunit beta type-6
+Macromolecule #15: Proteasome subunit beta type-7
+Macromolecule #16: Proteasome subunit beta type-3
+Macromolecule #17: Proteasome subunit beta type-2
+Macromolecule #18: Proteasome subunit beta type-5
+Macromolecule #19: Proteasome subunit beta type-1
+Macromolecule #20: Proteasome subunit beta type-4
+Macromolecule #21: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #22: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #24: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #27: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #28: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #29: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #30: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #31: 26S proteasome complex subunit SEM1
+Macromolecule #32: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #33: Substrate
+Macromolecule #34: Ubiquitin
+Macromolecule #35: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #38: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 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: 3.5 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
China, 1 items
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Z (Sec.)
Y (Row.)
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Processing
FIELD EMISSION GUN
