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- EMDB-2047: Structure of the human 26S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-2047
TitleStructure of the human 26S proteasome
Map dataThe deposited map has been supersampled to a grid of 1.412 angstroms (from the experimental 2.824 angstroms) for improved display
Sample
  • Sample: 26S proteasome
  • Protein or peptide: 26S proteasome
Keywords26S proteasome / proteasome / 20S / 19S / human
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
Authorsda Fonseca PCA / He J / Morris EP
CitationJournal: Mol Cell / Year: 2012
Title: Molecular model of the human 26S proteasome.
Authors: Paula C A da Fonseca / Jun He / Edward P Morris /
Abstract: The 26S proteasome plays a fundamental role in eukaryotic homeostasis by undertaking the highly controlled degradation of a wide range of proteins, including key cellular regulators such as those ...The 26S proteasome plays a fundamental role in eukaryotic homeostasis by undertaking the highly controlled degradation of a wide range of proteins, including key cellular regulators such as those controlling cell-cycle progression and apoptosis. Here we report the structure of the human 26S proteasome determined by cryo-electron microscopy and single-particle analysis, with secondary structure elements identified both in the 20S proteolytic core region and in the 19S regulatory particle. We have used this information together with crystal structures, homology models, and other biochemical information to construct a molecular model of the complete 26S proteasome. This model allows for a detailed description of the 20S core within the 26S proteasome and redefines the overall assignment of subunits within the 19S regulatory particle. The information presented here provides a strong basis for a mechanistic understanding of the 26S proteasome.
History
DepositionMar 8, 2012-
Header (metadata) releaseMar 30, 2012-
Map releaseApr 17, 2012-
UpdateApr 17, 2012-
Current statusApr 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDEP_2047.jpg

Downloads & links

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Map

FileDownload / File: emd_2047.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe deposited map has been supersampled to a grid of 1.412 angstroms (from the experimental 2.824 angstroms) for improved display
Voxel sizeX=Y=Z: 1.412 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-12.14980793 - 17.262060170000002
Average (Standard dev.)0.00000005 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-100-80
Dimensions360200160
Spacing360200160
CellA: 282.4 Å / B: 508.31998 Å / C: 225.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4121.4121.412
M x/y/z200360160
origin x/y/z0.0000.0000.000
length x/y/z282.400508.320225.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-100-180-80
NC/NR/NS200360160
D min/max/mean-12.15017.2620.000

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Supplemental data

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Sample components

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Entire : 26S proteasome

EntireName: 26S proteasome
Components
  • Sample: 26S proteasome
  • Protein or peptide: 26S proteasome

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Supramolecule #1000: 26S proteasome

SupramoleculeName: 26S proteasome / type: sample / ID: 1000 / Oligomeric state: dimer / Number unique components: 1
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: 26S proteasome

MacromoleculeName: 26S proteasome / type: protein_or_peptide / ID: 1 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Erythrocyte
Molecular weightTheoretical: 2.6 MDa

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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

Concentration0.15 mg/mL
BufferDetails: 50 mM Tris-HCl, pH 7.5, mM MgCl2, 2 mM ATP and 1 mM dithiotreitol
GridDetails: Quantifoil coated with thin layer of carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 5 seconds

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsCCD images binned x2
DateOct 20, 2010
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.475 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 63000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CCD frame
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: IMAGIC,Spider,in-house,software / Number images used: 12718

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