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- PDB-5vhr: Conformational Landscape of the p28-Bound Human Proteasome Regula... -

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Entry
Database: PDB / ID: 5vhr
TitleConformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 2
  • (26S proteasome regulatory subunit ...) x 6
KeywordsHYDROLASE / p28 / 26S proteasome / regulatory particle / 19S / gankyrin
Function / homology
Function and homology information


cytoplasmic sequestering of NF-kappaB / positive regulation of inclusion body assembly / proteasome regulatory particle assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity ...cytoplasmic sequestering of NF-kappaB / positive regulation of inclusion body assembly / proteasome regulatory particle assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / negative regulation of NF-kappaB transcription factor activity / negative regulation of MAPK cascade / regulation of protein catabolic process / negative regulation of release of cytochrome c from mitochondria / proteasome storage granule / negative regulation of DNA damage response, signal transduction by p53 class mediator / blastocyst development / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / general transcription initiation factor binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / enzyme regulator activity / : / inclusion body / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cytoskeletal protein binding / 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 / positive regulation of protein ubiquitination / 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 / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / protein localization to plasma membrane / Degradation of DVL / P-body / 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 / 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 / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cytoplasmic ribonucleoprotein granule / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
: / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Proteasomal ATPase OB C-terminal domain ...: / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Ankyrin repeat / ATPase family associated with various cellular activities (AAA) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ATPase, AAA-type, core / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Armadillo-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsLu, Y. / Wu, J. / Dong, Y. / Chen, S. / Sun, S. / Ma, Y.B. / Ouyang, Q. / Finley, D. / Kirschner, M.W. / Mao, Y.
CitationJournal: Mol Cell / Year: 2017
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
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
G: 26S proteasome non-ATPase regulatory subunit 10
A: 26S proteasome regulatory subunit 7
B: 26S proteasome regulatory subunit 4
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
C: 26S proteasome regulatory subunit 8
f: 26S proteasome non-ATPase regulatory subunit 2


Theoretical massNumber of molelcules
Total (without water)295,8458
Polymers295,8458
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13100 Å2
ΔGint-24 kcal/mol
Surface area127510 Å2

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Components

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26S proteasome non-ATPase regulatory subunit ... , 2 types, 2 molecules Gf

#1: Protein 26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin / p28(GANK)


Mass: 24142.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD10 / Production host: Homo sapiens (human) / References: UniProt: O75832
#8: Protein 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome ...26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 93790.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Production host: Homo sapiens (human) / References: UniProt: Q13200

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26S proteasome regulatory subunit ... , 6 types, 6 molecules ABDEFC

#2: Protein 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 29746.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC2, MSS1 / Production host: Homo sapiens (human) / References: UniProt: P35998
#3: Protein 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 29958.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC1 / Production host: Homo sapiens (human) / References: UniProt: P62191
#4: Protein 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 29497.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC4, MIP224, TBP7 / Production host: Homo sapiens (human) / References: UniProt: P43686
#5: Protein 26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 29434.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6, SUG2 / Production host: Homo sapiens (human) / References: UniProt: P62333
#6: Protein 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 29773.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC3, TBP1 / Production host: Homo sapiens (human) / References: UniProt: P17980
#7: Protein 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 29501.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Production host: Homo sapiens (human) / References: UniProt: P62195

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Proteasome regulatory particle / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14464 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03419603
ELECTRON MICROSCOPYf_angle_d1.68926435
ELECTRON MICROSCOPYf_dihedral_angle_d8.77512522
ELECTRON MICROSCOPYf_chiral_restr0.0753012
ELECTRON MICROSCOPYf_plane_restr0.0093458

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