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- EMDB-8662: Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Chann... -

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Entry
Database: EMDB / ID: 8662
TitleNucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome
Map dataFinal map corrected with a B-factor of -80
Sample26S proteasome bound to ATP-gammaS
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
Function / homologyProteasome beta subunits C terminal / Proteasome subunit alpha5 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit beta 6 / Proteasome subunit alpha4 / Proteasome subunit alpha2 ...Proteasome beta subunits C terminal / Proteasome subunit alpha5 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit beta 6 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome beta 3 subunit / Proteasome subunit beta 5 / Nucleophile aminohydrolases, N-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Proteasome, subunit alpha/beta / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / Proteasome subunit alpha 3 / Proteasome subunit / ABC-family proteins mediated transport / APC/C:Cdc20 mediated degradation of Securin / Separation of Sister Chromatids / Regulation of activated PAK-2p34 by proteasome mediated degradation / Downstream TCR signaling / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Proteasome subunit A N-terminal signature / 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 / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunits signature. / Proteasome alpha-type subunits signature. / Regulation of ornithine decarboxylase (ODC) / AUF1 (hnRNP D0) binds and destabilizes mRNA / Autodegradation of the E3 ubiquitin ligase COP1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / CDT1 association with the CDC6:ORC:origin complex / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / The role of GTSE1 in G2/M progression after G2 checkpoint / RUNX1 regulates transcription of genes involved in differentiation of HSCs / UCH proteinases / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / Neddylation / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Negative regulation of NOTCH4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Neutrophil degranulation / MAPK6/MAPK4 signaling / Defective CFTR causes cystic fibrosis / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / FCERI mediated NF-kB activation / purine ribonucleoside triphosphate binding / negative regulation of inflammatory response to antigenic stimulus / regulation of endopeptidase activity / immune system process / myofibril / NF-kappaB binding / polysome / proteasome complex / proteasome core complex, beta-subunit complex / proteasome core complex / proteasomal ubiquitin-independent protein catabolic process / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsZhu Y / Wang WL / Yu D / Ouyang Q / Lu Y / Mao Y
CitationJournal: Nat Commun / Year: 2018
Title: Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Authors: Yanan Zhu / Wei Li Wang / Daqi Yu / Qi Ouyang / Ying Lu / Youdong Mao
Validation ReportPDB-ID: 5vfo

SummaryFull reportAbout validation report
DateDeposition: Apr 8, 2017 / Header (metadata) release: Sep 20, 2017 / Map release: Jul 18, 2018 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vfo
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8662.map.gz (map file in CCP4 format, 702465 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
560 pix
0.75 Å/pix.
= 420. Å
560 pix
0.75 Å/pix.
= 420. Å
560 pix
0.75 Å/pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.012748035 - 0.02731222
Average (Standard dev.)0.000030307066 (0.001778131)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions560560560
Origin0.0.0.
Limit559.559.559.
Spacing560560560
CellA=B=C: 420.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.750.750.75
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0130.0270.000

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Supplemental data

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Sample components

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Entire 26S proteasome bound to ATP-gammaS

EntireName: 26S proteasome bound to ATP-gammaS / Number of components: 15

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Component #1: protein, 26S proteasome bound to ATP-gammaS

ProteinName: 26S proteasome bound to ATP-gammaS / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.727658 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.72526 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.118189 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Proteasome subunit alpha type-7

ProteinName: Proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.382178 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.569957 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.728428 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.2871 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 20.471129 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.745256 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.841701 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.720146 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.199072 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.578986 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #15: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.994324 kDa
SourceSpecies: Homo sapiens (human)
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: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Raw dataEMPIAR-10090 (Title: Nucleotide-Driven Triple-State Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome
Data size: 2.8 TB
Data #1: Motion-corrected single frame micrographs of ATP-gS-bound human proteasome [micrographs - single frame]
Data #2: Single-particle stacks of classified conformations [picked particles - multiframe - processed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 228086
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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