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- EMDB-6577: Cryo-EM map of yeast 26S proteasome in M2 state derived from Arct... -

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Basic information

Entry
Database: EMDB / ID: 6577
TitleCryo-EM map of yeast 26S proteasome in M2 state derived from Arctica dataset
Map dataReconstruction of single particle
Sampleyeast 26S proteasome in M2 state:
26S proteasome
Function / homologyProteasome beta 3 subunit / Rpn11/EIF3F, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Tetratricopeptide repeat / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Proteasome subunit Rpn10 / Proteasome subunit beta 4 ...Proteasome beta 3 subunit / Rpn11/EIF3F, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Tetratricopeptide repeat / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Proteasome subunit Rpn10 / Proteasome subunit beta 4 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit alpha2 / 26S proteasome regulatory subunit P45-like / Proteasome/cyclosome repeat / von Willebrand factor, type A / AAA+ ATPase domain / Ubiquitin interacting motif / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / 26S proteasome non-ATPase regulatory subunit Rpn12 / Armadillo-type fold / Proteasomal ubiquitin receptor Rpn13/ADRM1 / DSS1/SEM1 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat-containing domain / 26S proteasome regulatory subunit, C-terminal / Proteasome subunit alpha6 / Proteasome subunit alpha4 / Proteasome component (PCI) domain / PCI domain / Proteasome subunit alpha 7-like / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome/cyclosome repeat / Proteasome subunit alpha 3 / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome subunit beta Pre3 / MPN domain / Proteasome subunit alpha 1 / 26S Proteasome regulatory subunit 6B / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 8 / von Willebrand factor A-like domain superfamily / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Proteasome, subunit alpha/beta / JAB1/MPN/MOV34 metalloenzyme domain / Maintenance of mitochondrial structure and function / TNFR2 non-canonical NF-kB pathway / Proteasome alpha-type subunit profile. / Proteasome alpha-subunit, N-terminal domain / Proteasome beta-type subunit profile. / Cross-presentation of soluble exogenous antigens (endosomes) / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 / SCF(Skp2)-mediated degradation of p27/p21 / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / TPR repeat region circular profile. / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Antigen processing: Ubiquitination & Proteasome degradation / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome beta subunits C terminal / Proteasome beta-type subunits signature. / PCI domain profile.
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 8.3 Å resolution
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
DateDeposition: Jan 6, 2016 / Header (metadata) release: Mar 30, 2016 / Map release: May 11, 2016 / Last update: Jun 1, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.146
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.146
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6577.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2.54 Å/pix.
= 650.24 Å
256 pix
2.54 Å/pix.
= 650.24 Å
256 pix
2.54 Å/pix.
= 650.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level:0.146 (by author), 0.146 (movie #1):
Minimum - Maximum-0.16334881 - 0.36939761
Average (Standard dev.)0.00069428 (0.01684476)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 650.24 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z650.240650.240650.240
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1630.3690.001

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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 state / 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 proteasome / 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

ImagingMicroscope: OTHER / Date: Nov 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
LensMagnification: 78000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.6 - 3.2 nm
Specimen HolderModel: OTHER / Temperature: 100 K
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 6570
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: 16063
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: 8.3 Å / Resolution method: FSC 0.143, gold-standard

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