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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
SampleHuman 26S proteasome
SourceHomo sapiens / human
Map data
Methodsingle particle reconstruction, at 3.9 Å resolution
AuthorsSchweitzer A / Aufderheide A / Rudack T / Beck F
CitationProc. Natl. Acad. Sci. U.S.A., 2016, 113, 7816-7821

Proc. Natl. Acad. Sci. U.S.A., 2016, 113, 7816-7821 StrPapers
Structure of the human 26S proteasome at a resolution of 3.9 Å.
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
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
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  • 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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Supplemental images

Downloads & links

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Map

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

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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 package.

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

Specimen statecell
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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Output model

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