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- EMDB-0209: AAA-ATPase ring of PAN-proteasomes -

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Basic information

Entry
Database: EMDB / ID: EMD-0209
TitleAAA-ATPase ring of PAN-proteasomes
Map dataATPase ring of PAN in a PAN-proteasome
Sample
  • Complex: PAN-proteasome
    • Protein or peptide: Proteasome-activating nucleotidase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsPAN / Proteasome / AAA-ATPase / Archaea / HYDROLASE
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Proteasome-activating nucleotidase PAN / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Proteasome-activating nucleotidase PAN / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea) / Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.85 Å
AuthorsMajumder P / Rudack T
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.
History
DepositionAug 20, 2018-
Header (metadata) releaseDec 26, 2018-
Map releaseDec 26, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6he4
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0209.png

Downloads & links

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Map

FileDownload / File: emd_0209.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATPase ring of PAN in a PAN-proteasome
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.075444 - 0.106007785
Average (Standard dev.)0.000004003887 (±0.0015337322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 514.56 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0750.1060.000

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Supplemental data

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Sample components

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Entire : PAN-proteasome

EntireName: PAN-proteasome
Components
  • Complex: PAN-proteasome
    • Protein or peptide: Proteasome-activating nucleotidase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: PAN-proteasome

SupramoleculeName: PAN-proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 1.25 MDa

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Macromolecule #1: Proteasome-activating nucleotidase

MacromoleculeName: Proteasome-activating nucleotidase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Molecular weightTheoretical: 29.738418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KDPMVYGFEV EEKPEVSYED IGGLDVQIEE IREAVELPLL KPELFAEVGI EPPKGVLLYG PPGTGKTLLA KAVANQTRAT FIRVVGSEF VQKYIGEGAR LVREVFQLAK EKAPSIIFID ELDAIAARRT NSDTSGDREV QRTMMQLLAE LDGFDPRGDV K VIGATNRI ...String:
KDPMVYGFEV EEKPEVSYED IGGLDVQIEE IREAVELPLL KPELFAEVGI EPPKGVLLYG PPGTGKTLLA KAVANQTRAT FIRVVGSEF VQKYIGEGAR LVREVFQLAK EKAPSIIFID ELDAIAARRT NSDTSGDREV QRTMMQLLAE LDGFDPRGDV K VIGATNRI DILDPAILRP GRFDRIIEVP LPTFEGRIQI FKIHTRKMKL AEDVDFKELA RITEGASGAD IKAICTEAGM FA IREERAK VTMLDFTKAI EKVLKKTTPI

UniProtKB: Proteasome-activating nucleotidase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 82207
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6he4:
AAA-ATPase ring of PAN-proteasomes

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