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- EMDB-6575: Cryo-EM map of yeast 26S proteasome in M2 state derived from Tita... -

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Basic information

Entry
Database: EMDB / ID: EMD-6575
TitleCryo-EM map of yeast 26S proteasome in M2 state derived from Titan dataset
Map data
Sampleyeast 26S proteasome in M2 stateProteasome:
26S proteasomeProteasome
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 / nuclear proteasome complex / proteasome regulatory particle / COP9 signalosome / mitochondrial fission / histone deubiquitination / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / proteasome core complex assembly / peptide catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome core complex / isopeptidase activity / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome complex / proteasome assembly / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent ERAD pathway / mRNA export from nucleus / Neutrophil degranulation / enzyme regulator activity / TBP-class protein binding / nucleotide-excision repair / ubiquitin binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription elongation from RNA polymerase II promoter / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / metallopeptidase activity / regulation of cell cycle / negative regulation of DNA-binding transcription factor activity / ubiquitinyl hydrolase 1 / proteasome-mediated ubiquitin-dependent protein catabolic process / thiol-dependent deubiquitinase / positive regulation of DNA-binding transcription factor activity / ubiquitin-dependent protein catabolic process / chromatin remodeling / endopeptidase activity / protein deubiquitination / ATP hydrolysis activity / mRNA binding / protein domain specific binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 ...Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / 26S proteasome non-ATPase regulatory subunit 3 / Proteasome regulatory subunit C-terminal / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1_SEM1 / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / RPN1, N-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S Proteasome regulatory subunit 7 / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S Proteasome regulatory subunit 6B / Proteasome/cyclosome repeat / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 26S proteasome regulatory subunit P45-like / Proteasomal ATPase OB C-terminal domain / Maintenance of mitochondrial structure and function / Rpn11/EIF3F, C-terminal / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit beta Pre3 / Proteasome subunit beta 5 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 7 / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha 1 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome beta-type subunit, conserved site / Proteasome alpha-type subunits signature. / Proteasome subunit A N-terminal signature / von Willebrand factor, type A / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / MPN domain / MPN domain profile. / Proteasome alpha-type subunit profile. / Proteasome alpha-type subunit / Proteasome beta-type subunit profile. / Proteasome B-type subunit / AAA+ lid domain / AAA ATPase, AAA+ lid domain / Proteasome subunit / Proteasome, subunit alpha/beta / TPR repeat profile. / AAA-protein family signature. / ATPase, AAA-type, conserved site / TPR repeat region circular profile. / von Willebrand factor A-like domain superfamily / Tetratricopeptide repeat
Similarity search - Domain/homology
26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 8 homolog ...26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / Proteasome subunit beta type-1 / Probable proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6B homolog / Proteasome subunit beta type-6 / 26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-2 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLuan B / Huang XL / Wu JP / Shi YG / Wang F
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of an endogenous yeast 26S proteasome reveals two major conformational states.
Authors: Bai Luan / Xiuliang Huang / Jianping Wu / Ziqing Mei / Yiwei Wang / Xiaobin Xue / Chuangye Yan / Jiawei Wang / Daniel J Finley / Yigong Shi / Feng Wang /
Abstract: The eukaryotic proteasome mediates degradation of polyubiquitinated proteins. Here we report the single-particle cryoelectron microscopy (cryo-EM) structures of the endogenous 26S proteasome from ...The eukaryotic proteasome mediates degradation of polyubiquitinated proteins. Here we report the single-particle cryoelectron microscopy (cryo-EM) structures of the endogenous 26S proteasome from Saccharomyces cerevisiae at 4.6- to 6.3-Å resolution. The fine features of the cryo-EM maps allow modeling of 18 subunits in the regulatory particle and 28 in the core particle. The proteasome exhibits two distinct conformational states, designated M1 and M2, which correspond to those reported previously for the proteasome purified in the presence of ATP-γS and ATP, respectively. These conformations also correspond to those of the proteasome in the presence and absence of exogenous substrate. Structure-guided biochemical analysis reveals enhanced deubiquitylating enzyme activity of Rpn11 upon assembly of the lid. Our structures serve as a molecular basis for mechanistic understanding of proteasome function.
History
DepositionJan 6, 2016-
Header (metadata) releaseJun 15, 2016-
Map releaseJun 15, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jcp
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3jcp
  • Surface level: 0.095
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_6575.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 256 pix.
= 537.6 Å
2.1 Å/pix.
x 256 pix.
= 537.6 Å
2.1 Å/pix.
x 256 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density
Contour LevelBy AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum-0.1208187 - 0.29240051
Average (Standard dev.)0.00106918 (±0.01470171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1210.2920.001

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Supplemental data

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Sample components

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Entire yeast 26S proteasome in M2 state

EntireName: yeast 26S proteasome in M2 stateProteasome / Details: The sample was monodisperse / Number of Components: 1
MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa

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Component #1: protein, 26S proteasome

ProteinName: 26S proteasomeProteasome / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (natural)Location in cell: Cytoplasma

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 15 mg/mL
Buffer solution: 50mM Tris7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP
pH: 7.5
Support filmQuantifoil Cu R2.0/2.0 200 mesh
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Nov 2, 2015
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Illumination Mode: SPOT SCAN
LensMagnification: 75000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1.5 - 2.5 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 5517
Details: Every image is the average of 21 frames recorded by the direct electron detector

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 25151
Details: The particles were selected in RELION and manually checked. 3D classification and refinement were performed in RELION.
3D reconstructionSoftware: RELION / CTF correction: Each micrographs / Resolution: 4.6 Å / Resolution Method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: The domains were separately fitted in chimera and then manually checked in Coot. The final model is refined with Phenix.
Input PDB model: 4CR2
Output model

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