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

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Basic information

Entry
Database: EMDB / ID: EMD-0211
Title20S proteasome from Archaeoglobus fulgidus
Map data20S control
Sample
  • Complex: 20S proteasome
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta
KeywordsPAN / Proteasome / AAA-ATPase / Archaea / hydrolase
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / 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 B-type subunit ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 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: 0.08
  • Imaged by UCSF Chimera
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  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0211.png

Downloads & links

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Map

FileDownload / File: emd_0211.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S control
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: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.33946908 - 0.50904465
Average (Standard dev.)0.000008314035 (±0.0052294387)
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-0.3390.5090.000

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Supplemental data

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Sample components

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Entire : 20S proteasome

EntireName: 20S proteasome
Components
  • Complex: 20S proteasome
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta

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Supramolecule #1: 20S proteasome

SupramoleculeName: 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
Molecular weightTheoretical: 710 KDa

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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 DSM 4304 (archaea)
Molecular weightTheoretical: 26.333248 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY ...String:
ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY RDDLSFDDAM VLGLVAMGLS IESELVPENI EVGYVKVDDR TFKEVSPEEL KPYVERANER IRELLKK

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: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Archaeoglobus fulgidus DSM 4304 (archaea)
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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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: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 105384
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-6he7:
20S proteasome from Archaeoglobus fulgidus

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