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- EMDB-8143: nuclear ribo-nucleoprotein complex -

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Basic information

Database: EMDB / ID: 8143
Titlenuclear ribo-nucleoprotein complex
Samplenuclear ribo-nucleoprotein complex
SourceChaetomium thermophilum / fungus / thermophilic /
Map dataNone
Methodsingle particle reconstruction, at 7.3 Å resolution
AuthorsKornprobst M / Turk M / Kellner N / Cheng J / Flemming D / Kos-Braun IC / Kos M / Thoms M / Berninghausen O / Beckmann R / Hurt E
CitationCell, 2016, 166, 380-393

Cell, 2016, 166, 380-393 Yorodumi Papers
Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.
Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt

Validation ReportPDB-ID: 5jpq

SummaryFull reportAbout validation report
DateDeposition: Apr 5, 2016 / Header (metadata) release: Aug 3, 2016 / Map release: Aug 3, 2016 / Last update: Aug 3, 2016

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5jpq
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5jpq
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_8143.map.gz (map file in CCP4 format, 359662 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
448 pix
1.07 Å/pix.
= 478.464 Å
448 pix
1.07 Å/pix.
= 478.464 Å
448 pix
1.07 Å/pix.
= 478.464 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.068 Å
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.05605118 - 0.10664072
Average (Standard dev.)-0.000251965 (0.006865005)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 478.464 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z478.464478.464478.464
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0560.107-0.000

Supplemental data

Sample components

Entire nuclear ribo-nucleoprotein complex

EntireName: nuclear ribo-nucleoprotein complex / Number of components: 1

Component #1: protein, nuclear ribo-nucleoprotein complex

ProteinName: nuclear ribo-nucleoprotein complex / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum / fungus / thermophilic /

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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: 2.66 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43116
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

Atomic model buiding

Output model

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