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- EMDB-9215: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Basic information

Entry
Database: EMDB / ID: 9215
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Map dataState EA map of substrate-engaged human proteasome, low pass-filtered at 2.8 Angstrom, with amplitude corrected with a B-factor of -50
SampleProteasome:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 2.8 Å resolution
AuthorsMao YD
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao
DateDeposition: Oct 16, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 14, 2018 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9215.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
0.69 Å/pix.
= 411. Å
600 pix
0.69 Å/pix.
= 411. Å
600 pix
0.69 Å/pix.
= 411. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.685 Å
Density
Contour Level:0.012 (by author), 0.011 (movie #1):
Minimum - Maximum-0.015957573 - 0.040363714
Average (Standard dev.)0.000089725276 (0.0019719985)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.00.00.0
Limit599.0599.0599.0
Spacing600600600
CellA=B=C: 411.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6850.6850.685
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z411.000411.000411.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0160.0400.000

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Supplemental data

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Sample components

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Entire Proteasome

EntireName: Proteasome / Number of components: 1

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Component #1: protein, Proteasome

ProteinName: Proteasome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen 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: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 184848
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

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