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- EMDB-0213: PAN-proteasome in state 2 -

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Basic information

Entry
Database: EMDB / ID: 0213
TitlePAN-proteasome in state 2
Map dataPSC of PAN-proteasome in state 2
SamplePAN-proteasome:
20S-proteasome / (Proteasome-activating ...) x 2 / (Proteasome subunit ...) x 2 / (ligand) x 3
Function / homologyProteasome alpha subunit, archaeal / ATPase, AAA-type, core / Proteasomal ATPase OB C-terminal domain / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome-activating nucleotidase PAN / Proteasome B-type subunit / Proteasome alpha-type subunit / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit A N-terminal signature ...Proteasome alpha subunit, archaeal / ATPase, AAA-type, core / Proteasomal ATPase OB C-terminal domain / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome-activating nucleotidase PAN / Proteasome B-type subunit / Proteasome alpha-type subunit / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome subunit A N-terminal signature / Proteasome beta-type subunit, conserved site / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / AAA+ ATPase domain / Proteasome subunit / Proteasome, subunit alpha/beta / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / ATPase family associated with various cellular activities (AAA) / proteasome-activating nucleotidase complex / protein unfolding / 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 / ATPase activity / ATP binding / cytoplasm / Proteasome-activating nucleotidase / Proteasome subunit alpha / Proteasome subunit beta
Function and homology information
SourceArchaeoglobus fulgidus DSM 4304 (archaea) / Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Methodsingle particle reconstruction / cryo EM / 6.35 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: 6he9

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: 0.0075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6he9
  • Surface level: 0.0075
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0213.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:0.0075 (by author), 0.0075 (movie #1):
Minimum - Maximum-0.04830493 - 0.061207086
Average (Standard dev.)0.000026992147 (0.0016352007)
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-0.0480.0610.000

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Supplemental data

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Sample components

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Entire PAN-proteasome

EntireName: PAN-proteasome / Number of components: 9

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Component #1: protein, PAN-proteasome

ProteinName: PAN-proteasome / Recombinant expression: No
MassTheoretical: 1.25 MDa
SourceSpecies: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, 20S-proteasome

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

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Component #3: protein, Proteasome-activating nucleotidase (PAN)

ProteinName: Proteasome-activating nucleotidase (PAN) / Recombinant expression: No
SourceSpecies: Archaeoglobus fulgidus DSM 4304 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Proteasome subunit alpha

ProteinName: Proteasome subunit alpha / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 27.15616 kDa
SourceSpecies: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Proteasome subunit beta

ProteinName: Proteasome subunit beta / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 22.132283 kDa
SourceSpecies: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Proteasome-activating nucleotidase

ProteinName: Proteasome-activating nucleotidase / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 44.102977 kDa
SourceSpecies: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #9: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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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: C1 (asymmetric) / Number of projections: 46148
3D reconstructionSoftware: RELION / Resolution: 6.35 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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