+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32272 | |||||||||
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Title | Structure of USP14-bound human 26S proteasome in state EA1_UBL | |||||||||
Map data | Complete map of the human proteasome holoenzyme in state EA1_UBL, with the RP/CP low-pass filtered to 3.3/2.8 angstrom and sharpened by a B-factor of -30/0 | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of ERAD pathway / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / regulation of chemotaxis / meiosis I ...negative regulation of ERAD pathway / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / regulation of chemotaxis / meiosis I / purine ribonucleoside triphosphate binding / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / regulation of endopeptidase activity / 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 / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / Impaired BRCA2 binding to RAD51 / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / polyubiquitin modification-dependent protein binding / general transcription initiation factor binding / endopeptidase activator activity / NF-kappaB binding / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / P-body / stem cell differentiation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / double-strand break repair via homologous recombination / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhang S / Zou S / Yin D / Wu Z / Mao Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2022 Title: USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. Authors: Shuwen Zhang / Shitao Zou / Deyao Yin / Lihong Zhao / Daniel Finley / Zhaolong Wu / Youdong Mao / Abstract: Proteasomal degradation of ubiquitylated proteins is tightly regulated at multiple levels. A primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the deubiquitylating ...Proteasomal degradation of ubiquitylated proteins is tightly regulated at multiple levels. A primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the deubiquitylating enzyme ubiquitin-specific protease 14 (USP14), which reversibly binds the proteasome and confers the ability to edit and reject substrates. How USP14 is activated and regulates proteasome function remain unknown. Here we present high-resolution cryo-electron microscopy structures of human USP14 in complex with the 26S proteasome in 13 distinct conformational states captured during degradation of polyubiquitylated proteins. Time-resolved cryo-electron microscopy analysis of the conformational continuum revealed two parallel pathways of proteasome state transitions induced by USP14, and captured transient conversion of substrate-engaged intermediates into substrate-inhibited intermediates. On the substrate-engaged pathway, ubiquitin-dependent activation of USP14 allosterically reprograms the conformational landscape of the AAA-ATPase motor and stimulates opening of the core particle gate, enabling observation of a near-complete cycle of asymmetric ATP hydrolysis around the ATPase ring during processive substrate unfolding. Dynamic USP14-ATPase interactions decouple the ATPase activity from RPN11-catalysed deubiquitylation and kinetically introduce three regulatory checkpoints on the proteasome, at the steps of ubiquitin recognition, substrate translocation initiation and ubiquitin chain recycling. These findings provide insights into the complete functional cycle of the USP14-regulated proteasome and establish mechanistic foundations for the discovery of USP14-targeted therapies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32272.map.gz | 887.2 MB | EMDB map data format | |
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Header (meta data) | emd-32272-v30.xml emd-32272.xml | 62.4 KB 62.4 KB | Display Display | EMDB header |
Images | emd_32272.png | 76.4 KB | ||
Others | emd_32272_additional_1.map.gz emd_32272_additional_2.map.gz emd_32272_additional_3.map.gz emd_32272_additional_4.map.gz | 868.6 MB 893.3 MB 870.7 MB 892.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32272 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32272 | HTTPS FTP |
-Related structure data
Related structure data | 7w37MC 7w38C 7w39C 7w3aC 7w3bC 7w3cC 7w3fC 7w3gC 7w3hC 7w3iC 7w3jC 7w3kC 7w3mC M: atomic model generated by this map C: citing same article (ref.) |
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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_32272.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Complete map of the human proteasome holoenzyme in state EA1_UBL, with the RP/CP low-pass filtered to 3.3/2.8 angstrom and sharpened by a B-factor of -30/0 | ||||||||||||||||||||
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
-Additional map: Unfiltered, unsharpened raw map of the human proteasome...
File | emd_32272_additional_1.map | ||||||||||||
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Annotation | Unfiltered, unsharpened raw map of the human proteasome in state EA1_UBL after RP-masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of the human proteasome in state EA1 UBL...
File | emd_32272_additional_2.map | ||||||||||||
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Annotation | Map of the human proteasome in state EA1_UBL after RP-masked refinement, low-pass filtered to 3.3 angstrom and sharpened by a B-factor of -30 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered, unsharpened raw map of the human proteasome...
File | emd_32272_additional_3.map | ||||||||||||
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Annotation | Unfiltered, unsharpened raw map of the human proteasome in state EA1_UBL after CP-masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of the human proteasome in state EA1 UBL...
File | emd_32272_additional_4.map | ||||||||||||
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Annotation | Map of the human proteasome in state EA1_UBL after CP-masked refinement, low-pass filtered to 3.3 angstrom with no sharpening B-factor applied | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 26S proteasome
+Supramolecule #1: 26S proteasome
+Macromolecule #1: 26S protease regulatory subunit 7
+Macromolecule #2: 26S protease regulatory subunit 4
+Macromolecule #3: Isoform 2 of 26S proteasome regulatory subunit 8
+Macromolecule #4: 26S protease regulatory subunit 6B
+Macromolecule #5: 26S proteasome regulatory subunit 10B
+Macromolecule #6: 26S protease 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: Isoform Long of 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 non-ATPase regulatory subunit 2
+Macromolecule #32: Ubiquitin carboxyl-terminal hydrolase 14
+Macromolecule #33: 26S proteasome complex subunit DSS1
+Macromolecule #34: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-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: 5.0 µm / Nominal defocus min: 0.4 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 367235 |