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- EMDB-1733: Mechanism of Gate Opening in the 20S proteasome by the proteasoma... -

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Basic information

Entry
Database: EMDB / ID: EMD-1733
TitleMechanism of Gate Opening in the 20S proteasome by the proteasomal ATPases
Map dataArchaeal 20S proteasome with an open gate
Sample
  • Sample: Thermoplasma acidophilum 20S proteasome
  • Protein or peptide: archaeal 20S proteasome
Keywords20S proteasome from Thermoplasma acidophilum with an open gate
Function / homology
Function and homology information


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 / endopeptidase activity / 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 alpha-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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-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 speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsRabl J / Smith DM / Yu Y / Chang SC / Goldberg AL / Cheng Y
CitationJournal: Mol Cell / Year: 2008
Title: Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases.
Authors: Julius Rabl / David M Smith / Yadong Yu / Shih-Chung Chang / Alfred L Goldberg / Yifan Cheng /
Abstract: Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. ...Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. These ATPases contain a conserved C-terminal hydrophobic-tyrosine-X (HbYX) motif that triggers gate opening upon ATP binding. Using cryo-electron microscopy, we identified the sites in the archaeal 20S where PAN's C-terminal residues bind and determined the structures of the gate in its closed and open forms. Peptides containing the HbYX motif bind to 20S in the pockets between neighboring alpha subunits where they interact with conserved residues required for gate opening. This interaction induces a rotation in the alpha subunits and displacement of a reverse-turn loop that stabilizes the open-gate conformation. This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause alpha subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry.
History
DepositionMay 21, 2010-
Header (metadata) releaseJun 16, 2010-
Map releaseJun 16, 2010-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3c91
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd1733.tif

Downloads & links

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Map

FileDownload / File: emd_1733.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArchaeal 20S proteasome with an open gate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 144 pix.
= 197.028 Å		1.37 Å/pix.
x 144 pix.
= 197.028 Å		1.37 Å/pix.
x 144 pix.
= 197.028 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-4.97991 - 9.01826
Average (Standard dev.)0.000000000319803 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 197.028 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.368251.368251.36825
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z197.028197.028197.028
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-4.9809.0180.000

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Supplemental data

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Sample components

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Entire : Thermoplasma acidophilum 20S proteasome

EntireName: Thermoplasma acidophilum 20S proteasome
Components
  • Sample: Thermoplasma acidophilum 20S proteasome
  • Protein or peptide: archaeal 20S proteasome

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Supramolecule #1000: Thermoplasma acidophilum 20S proteasome

SupramoleculeName: Thermoplasma acidophilum 20S proteasome / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa

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Macromolecule #1: archaeal 20S proteasome

MacromoleculeName: archaeal 20S proteasome / type: protein_or_peptide / ID: 1 / Name.synonym: archaeal 20S proteasome / Number of copies: 14 / Oligomeric state: 4 rings of heptamer / Recombinant expression: Yes
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

GridDetails: 400 mesh Quantifoil grid
VitrificationCryogen name: NITROGEN / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side-entry cryoholder / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN

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Atomic model buiding 1

Initial modelPDB ID:

1ya7

RefinementSpace: REAL
Output model

PDB-3c91:
Thermoplasma acidophilum 20S proteasome with an open gate

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Atomic model buiding 2

Initial modelPDB ID:

1pma

RefinementSpace: REAL
Output model

PDB-3c91:
Thermoplasma acidophilum 20S proteasome with an open gate

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