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- EMDB-5616: Yeast 20S proteasome with C-terminal peptide of yeast Rpt1 -

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Basic information

Entry
Database: EMDB / ID: EMD-5616
TitleYeast 20S proteasome with C-terminal peptide of yeast Rpt1
Map data3D density map of yeast 20S proteasome core particle with GST tag added to the C-terminus of beta-2 subunit in complex with the C-terminal peptide of yeast Rpt6
Sample
  • Sample: Yeast 20S proteasome
  • Protein or peptide: 20S proteasome
KeywordsYeast 20S proteasome / C-terminal peptide / yeast Rpt1
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsLi X / Kim HM / Cheng Y
CitationJournal: Nature / Year: 2013
Title: Reconfiguration of the proteasome during chaperone-mediated assembly.
Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan ...Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan Cheng / Daniel Finley /
Abstract: The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting ...The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting into pockets of the α-ring. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit. Here we report that the base subassembly of the Saccharomyces cerevisiae proteasome, which includes the Rpt ring, forms a high-affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6 and Rpn14. Chaperone-mediated dissociation was abrogated by a non-hydrolysable ATP analogue, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α-pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3-pocket. Although the Rpt6 tail is not visualized within an α-pocket in mature proteasomes, it inserts into the α2/α3-pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme.
History
DepositionMar 21, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseMay 15, 2013-
UpdateJun 5, 2013-
Current statusJun 5, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5616_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5616.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D density map of yeast 20S proteasome core particle with GST tag added to the C-terminus of beta-2 subunit in complex with the C-terminal peptide of yeast Rpt6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 200 pix.
= 294. Å		1.47 Å/pix.
x 200 pix.
= 294. Å		1.47 Å/pix.
x 200 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-0.72278702 - 2.07709718
Average (Standard dev.)-0.02841983 (±0.16506153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.471.471.47
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.7232.077-0.028

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Supplemental data

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Sample components

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Entire : Yeast 20S proteasome

EntireName: Yeast 20S proteasome
Components
  • Sample: Yeast 20S proteasome
  • Protein or peptide: 20S proteasome

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Supramolecule #1000: Yeast 20S proteasome

SupramoleculeName: Yeast 20S proteasome / type: sample / ID: 1000 / Oligomeric state: 28mer / Number unique components: 1
Molecular weightExperimental: 700 KDa

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Macromolecule #1: 20S proteasome

MacromoleculeName: 20S proteasome / type: protein_or_peptide / ID: 1 / Details: GST tag was added to C-terminus of beta-2 subunit / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 700 KDa

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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: Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsLow-dose procedure
DateJan 1, 2010
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 25 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 100000
Sample stageSpecimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsFREALIGN
CTF correctionDetails: Each Particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 51135

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Atomic model buiding 1

Initial modelPDB ID:

1ryp

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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