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- EMDB-32278: Structure of USP14-bound human 26S proteasome in substrate-engage... -
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Open data
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Basic information
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Title | Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_USP14 | |||||||||
![]() | Complete map of the human proteasome holoenzyme in state ED1_USP14, with the RP/CP low-pass filtered to 3.9/3.0 angstrom and sharpened by a B-factor of -20/0 | |||||||||
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Function / homology | ![]() 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 / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / deubiquitinase activity ...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 / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / deubiquitinase activity / regulation of chemotaxis / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / regulation of endopeptidase activity / negative regulation of programmed cell death / hypothalamus gonadotrophin-releasing hormone neuron development / 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) / female meiosis I / proteasome core complex / positive regulation of protein monoubiquitination / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / mitochondrion transport along microtubule / fat pad development / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / endopeptidase inhibitor activity / immune system process / myofibril / proteasome binding / female gonad development / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / proteasome storage granule / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Presynaptic phase of homologous DNA pairing and strand exchange / transcription factor binding / blastocyst development / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / proteasome assembly / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of ubiquitin-dependent protein catabolic process / mRNA export from nucleus / enzyme regulator activity / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / inclusion body / Maturation of protein E / Maturation of protein E / negative regulation of inflammatory response to antigenic stimulus / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / : / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Zhang S / Zou S / Yin D / Wu Z / Mao Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 890 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 70.7 KB 70.7 KB | Display Display | ![]() |
Images | ![]() | 75.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 897 MB 895.1 MB 871.9 MB 872 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w3fMC ![]() 7w37C ![]() 7w38C ![]() 7w39C ![]() 7w3aC ![]() 7w3bC ![]() 7w3cC ![]() 7w3gC ![]() 7w3hC ![]() 7w3iC ![]() 7w3jC ![]() 7w3kC ![]() 7w3mC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Complete map of the human proteasome holoenzyme in state ED1_USP14, with the RP/CP low-pass filtered to 3.9/3.0 angstrom and sharpened by a B-factor of -20/0 | ||||||||||||||||||||
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: Map of the human proteasome in state ED1 USP14...
File | emd_32278_additional_1.map | ||||||||||||
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Annotation | Map of the human proteasome in state ED1_USP14 after CP-masked refinement, low-pass filtered to 3.0 angstrom with no sharpening B-factor applied | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of the human proteasome in state ED1 USP14...
File | emd_32278_additional_2.map | ||||||||||||
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Annotation | Map of the human proteasome in state ED1_USP14 after RP-masked refinement, low-pass filtered to 3.9 angstrom and sharpened by a B-factor of -20 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered, unsharpened raw map of the human proteasome...
File | emd_32278_additional_3.map | ||||||||||||
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Annotation | Unfiltered, unsharpened raw map of the human proteasome in state ED1_USP14 after RP-masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered, unsharpened raw map of the human proteasome...
File | emd_32278_additional_4.map | ||||||||||||
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Annotation | Unfiltered, unsharpened raw map of the human proteasome in state ED1_USP14 after CP-masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 26S proteasome
+Supramolecule #1: 26S proteasome
+Supramolecule #2: 26S proteasome
+Supramolecule #3: substrate
+Supramolecule #4: USP14
+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 11
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #24: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #27: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #28: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #29: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #30: Substrate
+Macromolecule #31: Ubiquitin carboxyl-terminal hydrolase 14
+Macromolecule #32: Ubiquitin
+Macromolecule #33: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #34: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #35: 26S proteasome complex subunit DSS1
+Macromolecule #36: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #38: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | 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 | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124597 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |