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- EMDB-0212: PAN-proteasome in state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0212
TitlePAN-proteasome in state 1
Map dataPseudo-single capped PAN-proteasome in state 1
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
  • 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 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 ...proteasome-activating nucleotidase complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / 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 / proteasome-mediated 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-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: 6.86 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: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6he8
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0212.png

Downloads & links

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Map

FileDownload / File: emd_0212.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudo-single capped PAN-proteasome in state 1
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: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.03647783 - 0.043262266
Average (Standard dev.)0.000027298773 (±0.0013231856)
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-0.0360.0430.000

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Supplemental data

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Additional map: AAAob of PAN-proteasome in state 1

Fileemd_0212_additional.map
AnnotationAAAob of PAN-proteasome in state 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
  • 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-#3
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
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)

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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)

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Macromolecule #1: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 14 / 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: 27.15616 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QMGYDRAITV FSPDGRLFQV EYAREAVKRG ATAIGIKCKE GVILIADKRV GSKLLEADTI EKIYKIDEHI CAATSGLVAD ARVLIDRAR IEAQINRLTY DEPITVKELA KKICDFKQQY TQYGGVRPFG VSLLIAGVDE VPKLYETDPS GALLEYKATA I GMGRNAVT ...String:
QMGYDRAITV FSPDGRLFQV EYAREAVKRG ATAIGIKCKE GVILIADKRV GSKLLEADTI EKIYKIDEHI CAATSGLVAD ARVLIDRAR IEAQINRLTY DEPITVKELA KKICDFKQQY TQYGGVRPFG VSLLIAGVDE VPKLYETDPS GALLEYKATA I GMGRNAVT EFFEKEYRDD LSFDDAMVLG LVAMGLSIES ELVPENIEVG YVKVDDRTFK EVSPEELKPY VERANERIRE LL KK

UniProtKB: Proteasome subunit alpha

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Macromolecule #2: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 14 / 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: 22.132283 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD ...String:
TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD SASGDGIDVV KITEDEFYQY SPEEVEQILA KFRK

UniProtKB: Proteasome subunit beta

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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: 44.102977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LLEKLKKLEE DYYKLRELYR RLEDEKKFIE SERIRYEREV RRLRSEVERL RSPPLLVGVV SDILEDGRVV VKSSTGPKFV VNTSQYINE EELKPGARVA LNQQTLAIVN VLPTSKDPMV YGFEVEEKPE VSYEDIGGLD VQIEEIREAV ELPLLKPELF A EVGIEPPK ...String:
LLEKLKKLEE DYYKLRELYR RLEDEKKFIE SERIRYEREV RRLRSEVERL RSPPLLVGVV SDILEDGRVV VKSSTGPKFV VNTSQYINE EELKPGARVA LNQQTLAIVN VLPTSKDPMV YGFEVEEKPE VSYEDIGGLD VQIEEIREAV ELPLLKPELF A EVGIEPPK GVLLYGPPGT GKTLLAKAVA NQTRATFIRV VGSEFVQKYI GEGARLVREV FQLAKEKAPS IIFIDELDAI AA RRTNSDT SGDREVQRTM MQLLAELDGF DPRGDVKVIG ATNRIDILDP AILRPGRFDR IIEVPLPTFE GRIQIFKIHT RKM KLAEDV DFKELARITE GASGADIKAI CTEAGMFAIR EERAKVTMLD FTKAIEKVLK KTTPIPDLKG VMFV

UniProtKB: Proteasome-activating nucleotidase

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / 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 #5: MAGNESIUM ION

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

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / 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: 6.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 38230
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-6he8:
PAN-proteasome in state 1

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