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- EMDB-8684: Conformational Landscape of the p28-Bound Human Proteasome Regula... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8684 | |||||||||
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Title | Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle | |||||||||
![]() | p28-Bound Human Proteasome Regulatory Particle | |||||||||
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![]() | p28 / 26S proteasome / regulatory particle / 19S / gankyrin / HYDROLASE | |||||||||
Function / homology | ![]() positive regulation of inclusion body assembly / 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 / integrator complex / meiosis I / positive regulation of proteasomal protein catabolic process ...positive regulation of inclusion body assembly / 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 / integrator complex / 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 / negative regulation of programmed cell death / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / transcription factor binding / blastocyst development / general transcription initiation factor binding / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ERAD pathway / inclusion body / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / stem cell differentiation / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / P-body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / double-strand break repair via nonhomologous end joining / cytoplasmic ribonucleoprotein granule / Regulation of RAS by GAPs Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
![]() | Lu Y / Wu J | |||||||||
![]() | ![]() Title: Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle. Authors: Ying Lu / Jiayi Wu / Yuanchen Dong / Shuobing Chen / Shuangwu Sun / Yong-Bei Ma / Qi Ouyang / Daniel Finley / Marc W Kirschner / Youdong Mao / ![]() ![]() Abstract: The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of ...The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 92.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.9 KB 35.9 KB | Display Display | ![]() |
Images | ![]() | 69.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vhsMC ![]() 8672C ![]() 8674C ![]() 8675C ![]() 8676C ![]() 8677C ![]() 8678C ![]() 8679C ![]() 8680C ![]() 8681C ![]() 8682C ![]() 8683C ![]() 5vgzC ![]() 5vhfC ![]() 5vhhC ![]() 5vhiC ![]() 5vhjC ![]() 5vhmC ![]() 5vhnC ![]() 5vhoC ![]() 5vhpC ![]() 5vhqC ![]() 5vhrC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 70.0 Data #1: Classified single-particle datasets for multiple conformations of p28-bound human regulatory complex [picked particles - multiframe - processed]) |
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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 | p28-Bound Human Proteasome Regulatory Particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Proteasome regulatory particle
+Supramolecule #1: Proteasome regulatory particle
+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: 26S proteasome regulatory subunit 10B
+Macromolecule #6: 26S proteasome regulatory subunit 6A
+Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #11: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #12: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #13: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #14: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #17: 26S proteasome complex subunit SEM1
+Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #19: 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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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: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21885 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |