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- EMDB-8683: Conformational Landscape of the p28-Bound Human Proteasome Regula... -

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Entry
Database: EMDB / ID: 8683
TitleConformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
Map dataFinal Map of Rpn1-p28-AAA subcomplex in the TA7 state, corrected with a B-factor of -400
SampleProteasome regulatory particle
  • (26S proteasome non-ATPase regulatory subunit ...) x 2
  • (26S proteasome regulatory subunit ...) x 6
Function / homologyP-loop containing nucleoside triphosphate hydrolase / Ankyrin repeat / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / Cross-presentation of soluble exogenous antigens (endosomes) / ER-Phagosome pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...P-loop containing nucleoside triphosphate hydrolase / Ankyrin repeat / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / Cross-presentation of soluble exogenous antigens (endosomes) / ER-Phagosome pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Activation of NF-kappaB in B cells / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / AAA-protein family signature. / Ankyrin repeats (3 copies) / Proteasome/cyclosome repeat / ATPase family associated with various cellular activities (AAA) / Vif-mediated degradation of APOBEC3G / Ankyrin repeat-containing domain superfamily / 26S proteasome regulatory subunit 10B / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 4 / Ankyrin repeat-containing domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / Armadillo-type fold / Armadillo-like helical / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / Vpu mediated degradation of CD4 / SCF(Skp2)-mediated degradation of p27/p21 / Ankyrin repeat / Degradation of GLI1 by the proteasome / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin / CDT1 association with the CDC6:ORC:origin complex / Neutrophil degranulation / Ub-specific processing proteases / UCH proteinases / MAPK6/MAPK4 signaling / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Regulation of RAS by GAPs / Hedgehog 'on' state / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / CLEC7A (Dectin-1) signaling / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Downstream TCR signaling / Regulation of activated PAK-2p34 by proteasome mediated degradation / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of ornithine decarboxylase (ODC) / AUF1 (hnRNP D0) binds and destabilizes mRNA / Dectin-1 mediated noncanonical NF-kB signaling / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / AAA+ ATPase domain / Proteasome/cyclosome repeat / G2/M Checkpoints / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Antigen processing: Ubiquitination & Proteasome degradation / Interleukin-1 signaling / Regulation of expression of SLITs and ROBOs / Neddylation / Regulation of PTEN stability and activity / Regulation of RUNX3 expression and activity / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Ubiquitin-dependent degradation of Cyclin D1 / The role of GTSE1 in G2/M progression after G2 checkpoint / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / cytoplasmic sequestering of NF-kappaB / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / proteasome regulatory particle assembly / proteasome regulatory particle / proteasome accessory complex / proteasome-activating ATPase activity / nuclear proteasome complex / proteasome regulatory particle, base subcomplex / blastocyst development / intermediate filament cytoskeleton / cytosolic proteasome complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of programmed cell death / negative regulation of MAPK cascade / enzyme regulator activity / regulation of protein catabolic process
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 7.7 Å resolution
AuthorsLu Y / Wu J
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.
Validation ReportPDB-ID: 5vhr

SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Aug 23, 2017 / Last update: Aug 23, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vhr
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8683.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
0.86 Å/pix.
= 309.6 Å
360 pix
0.86 Å/pix.
= 309.6 Å
360 pix
0.86 Å/pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour Level:0.004 (by author), 0.004 (movie #1):
Minimum - Maximum-0.006379295 - 0.019442225
Average (Standard dev.)-0.00013668333 (0.0008392264)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0060.019-0.000

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Supplemental data

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Sample components

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Entire Proteasome regulatory particle

EntireName: Proteasome regulatory particle / Number of components: 9

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Component #1: protein, Proteasome regulatory particle

ProteinName: Proteasome regulatory particle / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, 26S proteasome non-ATPase regulatory subunit 10

ProteinName: 26S proteasome non-ATPase regulatory subunit 10 / Recombinant expression: No
MassTheoretical: 24.14249 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 26S proteasome regulatory subunit 7

ProteinName: 26S proteasome regulatory subunit 7 / Recombinant expression: No
MassTheoretical: 29.746465 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, 26S proteasome regulatory subunit 4

ProteinName: 26S proteasome regulatory subunit 4 / Recombinant expression: No
MassTheoretical: 29.958395 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 26S proteasome regulatory subunit 6B

ProteinName: 26S proteasome regulatory subunit 6B / Recombinant expression: No
MassTheoretical: 29.497975 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 26S proteasome regulatory subunit 10B

ProteinName: 26S proteasome regulatory subunit 10B / Recombinant expression: No
MassTheoretical: 29.434889 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Recombinant expression: No
MassTheoretical: 29.773246 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, 26S proteasome regulatory subunit 8

ProteinName: 26S proteasome regulatory subunit 8 / Recombinant expression: No
MassTheoretical: 29.501363 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, 26S proteasome non-ATPase regulatory subunit 2

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Recombinant expression: No
MassTheoretical: 93.790188 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Raw dataEMPIAR-10091 (Title: Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
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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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 14464
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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