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- EMDB-47726: Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rp... -
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Basic information
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Title | Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt2 at top of spiral staircase and partially unfolded Eos | |||||||||
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![]() | 26S Proteasome / MOTOR PROTEIN / HYDROLASE-PROTEIN BINDING complex | |||||||||
Function / homology | ![]() protein modification by small protein conjugation / positive regulation of inclusion body assembly / disulfide oxidoreductase activity / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / myeloid dendritic cell differentiation / cytosolic proteasome complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases ...protein modification by small protein conjugation / positive regulation of inclusion body assembly / disulfide oxidoreductase activity / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / myeloid dendritic cell differentiation / cytosolic proteasome complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / meiosis I / proteasome regulatory particle / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / aggresome assembly / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / negative regulation of programmed cell death / protein K63-linked deubiquitination / RHOBTB1 GTPase cycle / Regulation of ornithine decarboxylase (ODC) / RND1 GTPase cycle / RND2 GTPase cycle / Proteasome assembly / RND3 GTPase cycle / aggresome / 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 / Cross-presentation of soluble exogenous antigens (endosomes) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / regulation of mitotic cell cycle phase transition / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Somitogenesis / K63-linked deubiquitinase activity / RHOV GTPase cycle / Impaired BRCA2 binding to RAD51 / proteasome binding / transcription factor binding / regulation of protein catabolic process / myofibril / proteasome storage granule / RHOU GTPase cycle / Presynaptic phase of homologous DNA pairing and strand exchange / protein-disulfide reductase activity / response to tumor necrosis factor / general transcription initiation factor binding / response to type II interferon / blastocyst development / polyubiquitin modification-dependent protein binding / immune system process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / endopeptidase activator activity / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / mRNA export from nucleus / RHOBTB2 GTPase cycle / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / inclusion body / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / proteasome complex / proteolysis involved in protein catabolic process / bioluminescence / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / generation of precursor metabolites and energy / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / stem cell differentiation / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Arkinson C / Gee CL / Martin A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1. Authors: Connor Arkinson / Christine L Gee / Zeyuan Zhang / Ken C Dong / Andreas Martin / ![]() Abstract: The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting ...The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and sub-stoichiometric concentrations by time resolved cryo-EM. We identified distinct binding modes of TXNL1 that depend on the proteasome conformational and ATPase motor states. Together with biophysical and biochemical experiments, our structural studies reveal that the resting-state proteasome prior to substrate engagement with the ATPase motor binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, the actively degrading proteasome shows additional interactions leading to high-affinity TXNL1 binding, whereby TXNL1's C-terminal tail covers the catalytic groove of the Rpn11 deubiquitinase and coordinates the active-site Zn. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in all registers of spiral-staircase arrangements and thus visualize the complete ATP-hydrolysis cycle of the AAA+ motor, indicating temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the beta-barrel mEos3.2 substrate while the ATPase hexamer is in a particular spiral staircase register. Our findings challenge current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct but broad range of conformational states to coordinate cofactor binding and substrate processing. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 141.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 62.8 KB 62.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 172.2 KB | ||
Filedesc metadata | ![]() | 15.8 KB | ||
Others | ![]() ![]() ![]() ![]() | 75.6 MB 134.8 MB 139.2 MB 139.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9e8oMC ![]() 9e8gC ![]() 9e8hC ![]() 9e8iC ![]() 9e8jC ![]() 9e8kC ![]() 9e8lC ![]() 9e8nC ![]() 9e8qC 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
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_47726_additional_1.map | ||||||||||||
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-Additional map: DeepEMhancer sharpened map
File | emd_47726_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_47726_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_47726_half_map_2.map | ||||||||||||
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Sample components
+Entire : Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
+Supramolecule #1: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
+Macromolecule #1: 26S proteasome regulatory subunit 4
+Macromolecule #2: 26S protease regulatory subunit 8
+Macromolecule #3: 26S proteasome regulatory subunit 6B
+Macromolecule #4: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #5: Proteasome subunit alpha type-6
+Macromolecule #6: Proteasome subunit alpha type-2
+Macromolecule #7: Proteasome subunit alpha type-4
+Macromolecule #8: Proteasome subunit alpha type-7
+Macromolecule #9: Proteasome subunit alpha type-5
+Macromolecule #10: Proteasome subunit alpha type-1
+Macromolecule #11: Proteasome subunit alpha type-3
+Macromolecule #12: Proteasome subunit beta type-6
+Macromolecule #13: Proteasome subunit beta type-7
+Macromolecule #14: Proteasome subunit beta type-3
+Macromolecule #15: Proteasome subunit beta type-2
+Macromolecule #16: Proteasome subunit beta type-5
+Macromolecule #17: Proteasome subunit beta type-1
+Macromolecule #18: Proteasome subunit beta type-4
+Macromolecule #19: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #20: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #21: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #22: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #24: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #27: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #28: 26S proteasome complex subunit SEM1
+Macromolecule #29: 26S proteasome regulatory subunit 7
+Macromolecule #30: 26S proteasome regulatory subunit 6A
+Macromolecule #31: 26S protease regulatory subunit 10B
+Macromolecule #32: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #33: Ubiquitin,Green to red photoconvertible GFP-like protein EosFP
+Macromolecule #34: Thioredoxin-like protein 1
+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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Details: 30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP |
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k 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: 1.7 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |