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- EMDB-8335: Structural basis for dynamic regulation of the human 26S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-8335
TitleStructural basis for dynamic regulation of the human 26S proteasome
Map data
Sample26S proteasome holoenzymeProteasome
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / regulation of endopeptidase activity ...purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / regulation of endopeptidase activity / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / negative regulation of programmed cell death / myofibril / proteasome binding / blastocyst development / polyubiquitin modification-dependent protein binding / regulation of protein catabolic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / NIK/NF-kappaB signaling / negative regulation of G2/M transition of mitotic cell cycle / proteasome storage granule / Wnt signaling pathway, planar cell polarity pathway / proteasomal protein catabolic process / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / NF-kappaB binding / endopeptidase activator activity / proteasome core complex / regulation of hematopoietic stem cell differentiation / isopeptidase activity / regulation of mitotic cell cycle phase transition / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / stem cell differentiation / proteasome core complex, alpha-subunit complex / proteasome assembly / regulation of cellular amino acid metabolic process / threonine-type endopeptidase activity / polysome / ciliary basal body / ubiquitin-dependent ERAD pathway / sarcomere / inclusion body / mRNA export from nucleus / response to organonitrogen compound / TBP-class protein binding / regulation of proteasomal protein catabolic process / enzyme regulator activity / pre-replicative complex assembly / proteolysis involved in cellular protein catabolic process / osteoblast differentiation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / P-body / modulation of chemical synaptic transmission / tumor necrosis factor-mediated signaling pathway / response to virus / negative regulation of neuron death / cytoplasmic ribonucleoprotein granule / lipopolysaccharide binding / double-strand break repair via homologous recombination / response to organic cyclic compound / protein-macromolecule adaptor activity / nuclear matrix / metallopeptidase activity / protein K63-linked deubiquitination / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / postsynapse / azurophil granule lumen / positive regulation of canonical Wnt signaling pathway / negative regulation of canonical Wnt signaling pathway / anaphase-promoting complex-dependent catabolic process / negative regulation of inflammatory response to antigenic stimulus / proteasome-mediated ubiquitin-dependent protein catabolic process / stimulatory C-type lectin receptor signaling pathway / thiol-dependent deubiquitinase / Fc-epsilon receptor signaling pathway / regulation of mRNA stability / transmembrane transport / regulation of inflammatory response / double-strand break repair via nonhomologous end joining / post-translational protein modification / protein polyubiquitination / peptidase activity / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / secretory granule lumen / protein folding / response to oxidative stress / T cell receptor signaling pathway / response to ethanol / endopeptidase activity / blood microparticle / ficolin-1-rich granule lumen / nuclear body
26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome alpha-type subunit / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Peptidase T1A, proteasome beta-subunit / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome subunit alpha5 / Proteasome beta 3 subunit / CSN8/PSMD8/EIF3K ...26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome alpha-type subunit / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Peptidase T1A, proteasome beta-subunit / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome subunit alpha5 / Proteasome beta 3 subunit / CSN8/PSMD8/EIF3K / Proteasomal ATPase OB C-terminal domain / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Rpn11/EIF3F, C-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Proteasome subunit alpha4 / Armadillo-like helical / von Willebrand factor, type A / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Tetratricopeptide-like helical domain superfamily / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit, C-terminal / Proteasome/cyclosome repeat / Armadillo-type fold / Proteasome beta-type subunit, conserved site / Proteasome subunit beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome subunit beta 6 / AAA+ ATPase domain / 26S Proteasome non-ATPase regulatory subunit 14 / AAA ATPase, AAA+ lid domain / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / RPN1, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S proteasome regulatory subunit RPN2, C-terminal / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome subunit beta 5 / Proteasome subunit alpha 3 / MPN domain / von Willebrand factor A-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 26S Proteasome non-ATPase regulatory subunit 13 / Proteasome subunit alpha 1 / 26S Proteasome regulatory subunit 6A / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / Proteasome alpha-subunit, N-terminal domain / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 11 / Ubiquitin interacting motif
Proteasome subunit alpha type-6 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B ...Proteasome subunit alpha type-6 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 6 / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Proteasome subunit beta type-1 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / 26S proteasome non-ATPase regulatory subunit 13
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsChen S / Wu J / Lu Y / Ma YB / Lee BH / Yu Z / Ouyang Q / Finley D / Kirschner MW / Mao Y
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structural basis for dynamic regulation of the human 26S proteasome.
Authors: Shuobing Chen / Jiayi Wu / Ying Lu / Yong-Bei Ma / Byung-Hoon Lee / Zhou Yu / Qi Ouyang / Daniel J Finley / Marc W Kirschner / Youdong Mao /
Abstract: The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) ...The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitylated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. Using cryoelectron microscopy, we determined a near-atomic-resolution structure of the 2.5-MDa human proteasome in its ground state, as well as subnanometer-resolution structures of the holoenzyme in three alternative conformational states. The substrate-unfolding AAA-ATPase channel is narrowed by 10 inward-facing pore loops arranged into two helices that run in parallel with each other, one hydrophobic in character and the other highly charged. The gate of the core particle was unexpectedly found closed in the ground state and open in only one of the alternative states. Coordinated, stepwise conformational changes of the regulatory particle couple ATP hydrolysis to substrate translocation and regulate gating of the core particle, leading to processive degradation.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionAug 15, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseOct 19, 2016-
UpdateNov 30, 2016-
Current statusNov 30, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5t0h
  • Surface level: 0.0015
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8335.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å
0.86 Å/pix.
x 360 pix.
= 309.6 Å
0.86 Å/pix.
x 360 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 LevelBy AUTHOR: 0.0015 / Movie #1: 0.0015
Minimum - Maximum-0.0024096896 - 0.005274156
Average (Standard dev.)-0.000008824916 (±0.0005034961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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-54-3-120
NX/NY/NZ12323205
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0020.005-0.000

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Supplemental data

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Sample components

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Entire 26S proteasome holoenzyme

EntireName: 26S proteasome holoenzymeProteasome / Number of components: 1

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Component #1: protein, 26S proteasome holoenzyme

ProteinName: 26S proteasome holoenzymeProteasome / Recombinant expression: No
MassExperimental: 2.5 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: blotted for 2 seconds, blotting force 3.

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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: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 21000.0 X (nominal), 28736.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 10367 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18443
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL / Overall bvalue: 150
Output model

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