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- EMDB-8663: Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Chann... -

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Entry
Database: EMDB / ID: 8663
TitleNucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome
Map dataFinal map of SD1 state corrected with a B-factor of -70
Sample26S proteasome bound to ATP-gammaS
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • sem1
  • (26S proteasome regulatory subunit ...) x 6
  • (ligand) x 2
Function / homologyProteasome subunit alpha4 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 8 / Winged helix-like DNA-binding domain superfamily ...Proteasome subunit alpha4 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 8 / Winged helix-like DNA-binding domain superfamily / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 14 / Winged helix DNA-binding domain superfamily / AAA+ ATPase domain / Proteasome/cyclosome repeat / Proteasome beta subunits C terminal / 26S proteasome subunit RPN7 / Proteasome subunit A N-terminal signature / CSN8/PSMD8/EIF3K family / Proteasome regulatory subunit C-terminal / Ubiquitin interaction motif / PCI domain / von Willebrand factor A-like domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Proteasome subunit beta 5 / Proteasome subunit alpha 3 / MPN domain / von Willebrand factor, type A / Ubiquitin interacting motif / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit beta 6 / P-loop containing nucleoside triphosphate hydrolase / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / Nucleophile aminohydrolases, N-terminal / Proteasome subunit Rpn10 / ATPase, AAA-type, core / Armadillo-type fold / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / 26S proteasome regulatory subunit, C-terminal / Proteasome beta-type subunit, conserved site / Rpn11/EIF3F, C-terminal / Proteasome subunit beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasome alpha-type subunits signature. / Regulation of RAS by GAPs / 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 / Hedgehog 'on' state / Neutrophil degranulation / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / Degradation of GLI1 by the proteasome / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Metalloprotease DUBs / CDT1 association with the CDC6:ORC:origin complex / AAA-protein family signature. / Regulation of RUNX3 expression and activity / Antigen processing: Ubiquitination & Proteasome degradation / Negative regulation of NOTCH4 signaling / Interleukin-1 signaling / Regulation of expression of SLITs and ROBOs / Neddylation / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.2 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: 5vfp

SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2017 / Header (metadata) release: Jul 18, 2018 / Map release: Jul 18, 2018 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vfp
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8663.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:0.008 (by author), 0.008 (movie #1):
Minimum - Maximum-0.010175013 - 0.022703705
Average (Standard dev.)0.000034475026 (0.0016657847)
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-0.0100.0230.000

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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: 35

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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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Component #16: protein, 26S proteasome non-ATPase regulatory subunit 1

ProteinName: 26S proteasome non-ATPase regulatory subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.26318 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #17: protein, 26S proteasome non-ATPase regulatory subunit 3

ProteinName: 26S proteasome non-ATPase regulatory subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.755656 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #18: protein, 26S proteasome non-ATPase regulatory subunit 12

ProteinName: 26S proteasome non-ATPase regulatory subunit 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.979359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #19: protein, 26S proteasome non-ATPase regulatory subunit 6

ProteinName: 26S proteasome non-ATPase regulatory subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.336906 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #20: protein, 26S proteasome non-ATPase regulatory subunit 7

ProteinName: 26S proteasome non-ATPase regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.382094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #21: protein, 26S proteasome non-ATPase regulatory subunit 13

ProteinName: 26S proteasome non-ATPase regulatory subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.619898 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #22: protein, 26S proteasome non-ATPase regulatory subunit 4

ProteinName: 26S proteasome non-ATPase regulatory subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.866023 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #23: protein, 26S proteasome non-ATPase regulatory subunit 14

ProteinName: 26S proteasome non-ATPase regulatory subunit 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.329355 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #24: protein, 26S proteasome non-ATPase regulatory subunit 8

ProteinName: 26S proteasome non-ATPase regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.039699 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #25: protein, sem1

ProteinName: sem1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.333191 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #26: protein, 26S proteasome non-ATPase regulatory subunit 11

ProteinName: 26S proteasome non-ATPase regulatory subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.868555 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #27: protein, 26S proteasome regulatory subunit 7

ProteinName: 26S proteasome regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.823457 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #28: protein, 26S proteasome regulatory subunit 4

ProteinName: 26S proteasome regulatory subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.890246 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #29: protein, 26S proteasome regulatory subunit 8

ProteinName: 26S proteasome regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.034086 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #30: protein, 26S proteasome regulatory subunit 6B

ProteinName: 26S proteasome regulatory subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.303543 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #31: protein, 26S proteasome regulatory subunit 10B

ProteinName: 26S proteasome regulatory subunit 10B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.548078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #32: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.378 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #33: protein, 26S proteasome non-ATPase regulatory subunit 2

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.313625 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #34: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #35: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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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: 1 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: 66246
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 7
Output model

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