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- EMDB-0210: 20S core particle of PAN-proteasomes -

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Basic information

Entry
Database: EMDB / ID: EMD-0210
Title20S core particle of PAN-proteasomes
Map data20S alpha-beta of PAN-proteasomes
Sample
  • Complex: PAN-proteasome
    • Complex: 20S-proteasome
      • Protein or peptide: Proteasome subunit alpha
      • Protein or peptide: Proteasome subunit beta
    • Complex: Proteasome-activating nucleotidase (PAN)
      • Protein or peptide: Proteasome-activating nucleotidase
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Proteasome-activating nucleotidase PAN / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. ...Proteasome-activating nucleotidase PAN / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / 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 / Proteasome subunit alpha / Proteasome subunit beta
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: 4.12 Å
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.
History
DepositionAug 20, 2018-
Header (metadata) releaseDec 26, 2018-
Map releaseDec 26, 2018-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0372
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0372
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6he5
  • Surface level: 0.0372
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0210.png

Downloads & links

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Map

FileDownload / File: emd_0210.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S alpha-beta of PAN-proteasomes
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.0372 / Movie #1: 0.0372
Minimum - Maximum-0.15713851 - 0.21711725
Average (Standard dev.)0.000009996114 (±0.0025153332)
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-0.1570.2170.000

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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
    • Complex: 20S-proteasome
      • Protein or peptide: Proteasome subunit alpha
      • Protein or peptide: Proteasome subunit beta
    • Complex: Proteasome-activating nucleotidase (PAN)
      • Protein or peptide: Proteasome-activating nucleotidase

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Supramolecule #1: PAN-proteasome

SupramoleculeName: PAN-proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.25 MDa

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Supramolecule #2: 20S-proteasome

SupramoleculeName: 20S-proteasome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Proteasome-activating nucleotidase (PAN)

SupramoleculeName: Proteasome-activating nucleotidase (PAN) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
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: 27.692828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHLPQMGYD RAITVFSPDG RLFQVEYARE AVKRGATAIG IKCKEGVILI ADKRVGSKLL EADTIEKIYK IDEHICAATS GLVADARVL IDRARIEAQI NRLTYDEPIT VKELAKKICD FKQQYTQYGG VRPFGVSLLI AGVDEVPKLY ETDPSGALLE Y KATAIGMG ...String:
MGHLPQMGYD RAITVFSPDG RLFQVEYARE AVKRGATAIG IKCKEGVILI ADKRVGSKLL EADTIEKIYK IDEHICAATS GLVADARVL IDRARIEAQI NRLTYDEPIT VKELAKKICD FKQQYTQYGG VRPFGVSLLI AGVDEVPKLY ETDPSGALLE Y KATAIGMG RNAVTEFFEK EYRDDLSFDD AMVLGLVAMG LSIESELVPE NIEVGYVKVD DRTFKEVSPE ELKPYVERAN ER IRELLKK

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Macromolecule #2: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
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: 23.149414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGTTTVGLVC KDGVVMATEK RATMGNFIAS KAAKKIYQIA DRMAMTTAGS VGDAQFLARI IKIEANLYEI RRERKPTVRA IATLTSNLL NSYRYFPYLV QLLIGGIDSE GKSIYSIDPI GGAIEEKDIV ATGSGSLTAY GVLEDRFTPE IGVDEAVELA V RAIYSAMK ...String:
MGTTTVGLVC KDGVVMATEK RATMGNFIAS KAAKKIYQIA DRMAMTTAGS VGDAQFLARI IKIEANLYEI RRERKPTVRA IATLTSNLL NSYRYFPYLV QLLIGGIDSE GKSIYSIDPI GGAIEEKDIV ATGSGSLTAY GVLEDRFTPE IGVDEAVELA V RAIYSAMK RDSASGDGID VVKITEDEFY QYSPEEVEQI LAKFRKHHHH HH

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Macromolecule #3: Proteasome-activating nucleotidase

MacromoleculeName: Proteasome-activating nucleotidase / type: protein_or_peptide / ID: 3 / 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: 45.279219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMGGDSEIQ YLLEKLKKLE EDYYKLRELY RRLEDEKKFI ESERIRYERE VRRLRSEVER LRSPPLLVGV VSDILEDGRV VVKSSTGPK FVVNTSQYIN EEELKPGARV ALNQQTLAIV NVLPTSKDPM VYGFEVEEKP EVSYEDIGGL DVQIEEIREA V ELPLLKPE ...String:
GHMGGDSEIQ YLLEKLKKLE EDYYKLRELY RRLEDEKKFI ESERIRYERE VRRLRSEVER LRSPPLLVGV VSDILEDGRV VVKSSTGPK FVVNTSQYIN EEELKPGARV ALNQQTLAIV NVLPTSKDPM VYGFEVEEKP EVSYEDIGGL DVQIEEIREA V ELPLLKPE LFAEVGIEPP KGVLLYGPPG TGKTLLAKAV ANQTRATFIR VVGSEFVQKY IGEGARLVRE VFQLAKEKAP SI IFIDELD AIAARRTNSD TSGDREVQRT MMQLLAELDG FDPRGDVKVI GATNRIDILD PAILRPGRFD RIIEVPLPTF EGR IQIFKI HTRKMKLAED VDFKELARIT EGASGADIKA ICTEAGMFAI REERAKVTML DFTKAIEKVL KKTTPIPDLK GVMF V

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

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Image processing

CTF correctionSoftware - Name: MotionCorr2
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 182989

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6he5:
20S core particle of PAN-proteasomes

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