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- EMDB-4002: The human 26S proteasome at 3.9 -

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Basic information

Entry
Database: EMDB / ID: 4002
TitleThe human 26S proteasome at 3.9
Map data
SampleHuman 26S proteasome:
Function / homologyProteasome subunit alpha2 / 26S proteasome regulatory subunit 8 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 10B / 26S Proteasome regulatory subunit 6B / 26S Proteasome non-ATPase regulatory subunit 14 ...Proteasome subunit alpha2 / 26S proteasome regulatory subunit 8 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 10B / 26S Proteasome regulatory subunit 6B / 26S Proteasome non-ATPase regulatory subunit 14 / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / AAA+ ATPase domain / PCI domain / Proteasome subunit A N-terminal signature / CSN8/PSMD8/EIF3K family / Proteasome regulatory subunit C-terminal / DSS1/SEM1 family / Ubiquitin interaction motif / Proteasome/cyclosome repeat / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Winged helix DNA-binding domain superfamily / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Proteasome subunit beta 5 / Proteasome subunit alpha 3 / MPN domain / von Willebrand factor A-like domain superfamily / von Willebrand factor, type A / Ubiquitin interacting motif / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha4 / Proteasome subunit Rpn10 / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / P-loop containing nucleoside triphosphate hydrolase / Rpn11/EIF3F, C-terminal / ATPase, AAA-type, core / 26S proteasome regulatory subunit, C-terminal / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Proteasome beta subunit, C-terminal / Proteasome beta-type subunit, conserved site / Proteasome subunit beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Proteasome alpha-type subunit / Proteasome B-type subunit / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / Hedgehog 'on' state / UCH proteinases / MAPK6/MAPK4 signaling / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Regulation of RAS by GAPs / GLI3 is processed to GLI3R by the proteasome / Metalloprotease DUBs / Degradation of GLI2 by the proteasome / Degradation of GLI1 by the proteasome / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / Ub-specific processing proteases / Neutrophil degranulation / Degradation of DVL / Regulation of RUNX2 expression and activity / Antigen processing: Ubiquitination & Proteasome degradation / Interleukin-1 signaling / Regulation of expression of SLITs and ROBOs / Neddylation / Regulation of PTEN stability and activity / Regulation of RUNX3 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSchweitzer A / Aufderheide A / Rudack T / Beck F
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure of the human 26S proteasome at a resolution of 3.9 Å.
Authors: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister
Validation ReportPDB-ID: 5l4g

SummaryFull report
PDB-ID: 5l4k

SummaryFull report
About validation report
DateDeposition: May 25, 2016 / Header (metadata) release: Jun 22, 2016 / Map release: Jun 22, 2016 / Last update: Jul 26, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5l4g, PDB-5l4k
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5l4g
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5l4k
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4002.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.35 Å/pix.
= 518.4 Å
384 pix
1.35 Å/pix.
= 518.4 Å
384 pix
1.35 Å/pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.19493514 - 0.30707386
Average (Standard dev.)0.00031536914 (0.00694399)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 518.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1950.3070.000

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Supplemental data

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Sample components

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Entire Human 26S proteasome

EntireName: Human 26S proteasome / Number of components: 1
MassTheoretical: 2.5 MDa

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Component #1: protein, Human 26S proteasome

ProteinName: Human 26S proteasome / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: blood

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 1900 - nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 40211
Details: Images were collected in movie-mode at 33 frames/s.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 461402 / Details: Falcon III
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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