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- EMDB-3136: A Single Alpha Helix Drives Extensive Remodeling of the Proteasom... -

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Basic information

Entry
Database: EMDB / ID: EMD-3136
TitleA Single Alpha Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly
Map dataReconstruction of LP2
Sample
  • Sample: Recombinant LP2 (Lid Particle 2)
  • Protein or peptide: 26S proteasome regulatory subunit RPN3
  • Protein or peptide: 26S proteasome regulatory subunit RPN5
  • Protein or peptide: 26S proteasome regulatory subunit RPN6
  • Protein or peptide: 26S proteasome regulatory subunit RPN7
  • Protein or peptide: 26S proteasome regulatory subunit RPN8
  • Protein or peptide: 26S proteasome regulatory subunit RPN9
  • Protein or peptide: 26S proteasome regulatory subunit RPN11
  • Protein or peptide: 26S proteasome regulatory subunit Sem1
Keywordsproteasome / ubiquitin / proteolysis / electron microscopy / mass spectrometry
Function / homology
Function and homology information


protein deneddylation => GO:0000338 / molecular_function / SAGA complex localization to transcription regulatory region / : / proteasome storage granule assembly / transcription export complex 2 / peroxisome fission / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth ...protein deneddylation => GO:0000338 / molecular_function / SAGA complex localization to transcription regulatory region / : / proteasome storage granule assembly / transcription export complex 2 / peroxisome fission / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / regulation of protein catabolic process / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / protein deubiquitination / Ub-specific processing proteases / proteasome assembly / mRNA export from nucleus / enzyme regulator activity / Neutrophil degranulation / protein folding chaperone / proteasome complex / double-strand break repair via homologous recombination / metallopeptidase activity / ubiquitin-dependent protein catabolic process / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / structural molecule activity / positive regulation of transcription by RNA polymerase II / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Rpn9, C-terminal helix / Rpn9 C-terminal helix / ArsR-like helix-turn-helix domain / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome regulatory subunit, C-terminal / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal ...: / : / Rpn9, C-terminal helix / Rpn9 C-terminal helix / ArsR-like helix-turn-helix domain / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome regulatory subunit, C-terminal / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 7/8 / DSS1/SEM1 / DSS1/SEM1 / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1_SEM1 / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Rpn11/EIF3F, C-terminal / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / Proteasome component (PCI) domain / PCI domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / TPR repeat region circular profile. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / JAB1/MPN/MOV34 metalloenzyme domain / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit RPN3 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 16.0 Å
AuthorsTomko Jr RJ / Taylor DW / Chen ZA / Wang HW / Rappsilber J / Hochstrasser M
CitationJournal: Cell / Year: 2015
Title: A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly.
Authors: Robert J Tomko / David W Taylor / Zhuo A Chen / Hong-Wei Wang / Juri Rappsilber / Mark Hochstrasser /
Abstract: Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis ...Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis culminates with the joining of two large subcomplexes, the lid and base. In yeast and mammals, the lid appears to assemble completely before attaching to the base, but how this hierarchical assembly is enforced has remained unclear. Using biochemical reconstitutions, quantitative cross-linking/mass spectrometry, and electron microscopy, we resolve the mechanistic basis for the linkage between lid biogenesis and lid-base joining. Assimilation of the final lid subunit, Rpn12, triggers a large-scale conformational remodeling of the nascent lid that drives RP assembly, in part by relieving steric clash with the base. Surprisingly, this remodeling is triggered by a single Rpn12 α helix. Such assembly-coupled conformational switching is reminiscent of viral particle maturation and may represent a commonly used mechanism to enforce hierarchical assembly in multisubunit complexes.
History
DepositionAug 31, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseOct 21, 2015-
UpdateOct 21, 2015-
Current statusOct 21, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3136.png

Downloads & links

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Map

FileDownload / File: emd_3136.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of LP2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 160 pix.
= 448. Å		2.8 Å/pix.
x 160 pix.
= 448. Å		2.8 Å/pix.
x 160 pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-19.906469349999998 - 23.58402061
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-19.90623.584-0.000

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Supplemental data

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Sample components

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Entire : Recombinant LP2 (Lid Particle 2)

EntireName: Recombinant LP2 (Lid Particle 2)
Components
  • Sample: Recombinant LP2 (Lid Particle 2)
  • Protein or peptide: 26S proteasome regulatory subunit RPN3
  • Protein or peptide: 26S proteasome regulatory subunit RPN5
  • Protein or peptide: 26S proteasome regulatory subunit RPN6
  • Protein or peptide: 26S proteasome regulatory subunit RPN7
  • Protein or peptide: 26S proteasome regulatory subunit RPN8
  • Protein or peptide: 26S proteasome regulatory subunit RPN9
  • Protein or peptide: 26S proteasome regulatory subunit RPN11
  • Protein or peptide: 26S proteasome regulatory subunit Sem1

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Supramolecule #1000: Recombinant LP2 (Lid Particle 2)

SupramoleculeName: Recombinant LP2 (Lid Particle 2) / type: sample / ID: 1000 / Details: The sample was monodisperse.
Oligomeric state: 1 Rpn3: 1 Rpn5: 1 Rpn6: 1 Rpn7: 1 Rpn8: 1 Rpn9: 1 Rpn11: 1 Sem1
Number unique components: 8
Molecular weightTheoretical: 343 KDa

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Macromolecule #1: 26S proteasome regulatory subunit RPN3

MacromoleculeName: 26S proteasome regulatory subunit RPN3 / type: protein_or_peptide / ID: 1 / Name.synonym: RPN3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 64 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN3
GO: ubiquitin-dependent protein catabolic process, regulation of protein catabolic process, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: 26S proteasome regulatory subunit, C-terminal, Proteasome component (PCI) domain

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Macromolecule #2: 26S proteasome regulatory subunit RPN5

MacromoleculeName: 26S proteasome regulatory subunit RPN5 / type: protein_or_peptide / ID: 2 / Name.synonym: RPN5 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 52 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN5
GO: ubiquitin-dependent protein catabolic process, protein deneddylation => GO:0000338, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: Proteasome component (PCI) domain, ArsR-like helix-turn-helix domain

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Macromolecule #3: 26S proteasome regulatory subunit RPN6

MacromoleculeName: 26S proteasome regulatory subunit RPN6 / type: protein_or_peptide / ID: 3 / Name.synonym: RPN6 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 50 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN6
GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: Proteasome component (PCI) domain, INTERPRO: IPR013143

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Macromolecule #4: 26S proteasome regulatory subunit RPN7

MacromoleculeName: 26S proteasome regulatory subunit RPN7 / type: protein_or_peptide / ID: 4 / Name.synonym: RPN7 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 49 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN7
GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1, Proteasome component (PCI) domain, INTERPRO: IPR013026

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Macromolecule #5: 26S proteasome regulatory subunit RPN8

MacromoleculeName: 26S proteasome regulatory subunit RPN8 / type: protein_or_peptide / ID: 5 / Name.synonym: RPN8 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 38 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN8
GO: ubiquitin-dependent protein catabolic process, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: JAB1/MPN/MOV34 metalloenzyme domain, Rpn11/EIF3F, C-terminal

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Macromolecule #6: 26S proteasome regulatory subunit RPN9

MacromoleculeName: 26S proteasome regulatory subunit RPN9 / type: protein_or_peptide / ID: 6 / Name.synonym: RPN9 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 46 KDa
SequenceUniProtKB: 26S proteasome regulatory subunit RPN9
GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: Proteasome component (PCI) domain, ArsR-like helix-turn-helix domain

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Macromolecule #7: 26S proteasome regulatory subunit RPN11

MacromoleculeName: 26S proteasome regulatory subunit RPN11 / type: protein_or_peptide / ID: 7 / Name.synonym: RPN11 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 34 KDa
SequenceUniProtKB: Ubiquitin carboxyl-terminal hydrolase RPN11
GO: protein deubiquitination, mitochondrial fission, cysteine-type deubiquitinase activity, proteasome complex, proteasome regulatory particle, lid subcomplex
InterPro: JAB1/MPN/MOV34 metalloenzyme domain, Rpn11/EIF3F, C-terminal

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Macromolecule #8: 26S proteasome regulatory subunit Sem1

MacromoleculeName: 26S proteasome regulatory subunit Sem1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightTheoretical: 10 KDa
SequenceUniProtKB: 26S proteasome complex subunit SEM1
GO: proteasome complex, proteasome regulatory particle, lid subcomplex, proteasome-mediated ubiquitin-dependent protein catabolic process, proteasome assembly
InterPro: DSS1/SEM1

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.04 mg/mL
BufferpH: 7.5
Details: 50 mM Tris, 150 mM NaCl, 5 mM MgCl2, and 10% glycerol
StainingType: NEGATIVE
Details: Sample was negatively stained with six consecutive droplets of 2% uranyl acetate.
GridDetails: 400 mesh Cu grid with thin carbon, glow discharged with a sputter coater.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 20
DetailsData acquired using Leginon.
DateApr 26, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 600 / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX / Number images used: 60000

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