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- EMDB-0211: 20S proteasome from Archaeoglobus fulgidus -

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Basic information

Entry
Database: EMDB / ID: 0211
Title20S proteasome from Archaeoglobus fulgidusProteasome
Map data20S control
Sample20S proteasomeProteasome:
(Proteasome subunit ...) x 2
Function / homologyPeptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunits signature. / Proteasome alpha-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / Proteasome, subunit alpha/beta / Proteasome beta-type subunit, conserved site ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunits signature. / Proteasome alpha-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / Proteasome, subunit alpha/beta / Proteasome beta-type subunit, conserved site / Proteasome alpha subunit, archaeal / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunit / Proteasome B-type subunit / Nucleophile aminohydrolases, N-terminal / proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm / Proteasome subunit alpha / Proteasome subunit beta
Function and homology information
SourceArchaeoglobus fulgidus DSM 4304 (archaea)
Methodsingle particle reconstruction / cryo EM / 3.69 Å resolution
AuthorsMajumder P / Rudack T / Beck F / Baumeister W
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle.
Authors: Parijat Majumder / Till Rudack / Florian Beck / Radostin Danev / Günter Pfeifer / István Nagy / Wolfgang Baumeister
Abstract: Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein ...Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein homeostasis, and control vital cellular processes. While the eukaryotic 26S proteasome is extensively characterized, its putative evolutionary precursor, the archaeal proteasome, remains poorly understood. The primordial archaeal proteasome consists of a 20S proteolytic core particle (CP), and an AAA-ATPase module. This minimal complex degrades protein unassisted by non-ATPase subunits that are present in a 26S proteasome regulatory particle (RP). Using cryo-EM single-particle analysis, we determined structures of the archaeal CP in complex with the AAA-ATPase PAN (proteasome-activating nucleotidase). Five conformational states were identified, elucidating the functional cycle of PAN, and its interaction with the CP. Coexisting nucleotide states, and correlated intersubunit signaling features, coordinate rotation of the PAN-ATPase staircase, and allosterically regulate N-domain motions and CP gate opening. These findings reveal the structural basis for a sequential around-the-ring ATPase cycle, which is likely conserved in AAA-ATPases.
Validation ReportPDB-ID: 6he7

SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2018 / Header (metadata) release: Dec 26, 2018 / Map release: Dec 26, 2018 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6he7
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0211.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.34 Å/pix.
= 514.56 Å
384 pix
1.34 Å/pix.
= 514.56 Å
384 pix
1.34 Å/pix.
= 514.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.33946908 - 0.50904465
Average (Standard dev.)0.000008314035 (0.0052294387)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 514.56 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z514.560514.560514.560
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.3390.5090.000

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Supplemental data

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Sample components

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Entire 20S proteasome

EntireName: 20S proteasome / Number of components: 3

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Component #1: protein, 20S proteasome

ProteinName: 20S proteasomeProteasome / Recombinant expression: No
MassTheoretical: 710 kDa
SourceSpecies: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Proteasome subunit alpha

ProteinName: Proteasome subunit alpha / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 26.333248 kDa
SourceSpecies: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Proteasome subunit beta

ProteinName: Proteasome subunit beta / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 22.132283 kDa
SourceSpecies: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.1
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 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 processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C7 (7 fold cyclic) / Number of projections: 105384
3D reconstructionSoftware: RELION / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

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

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