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- EMDB-2453: 30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4a -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: 2453
Title30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4a
Map dataGroup 4a
Sample30S Reconstitution Reaction:
ribosome-prokaryote
KeywordsRibosome Assembly / 30S Ribosome Subunit / 30S Assembly / Time-resolved electron microscopy / Discovery Single-particle Profiling / 30S Ribosome Subunit Assembly Intermediate
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / 31.67 Å resolution
AuthorsMulder AM / Yoshioka C / Beck A / Bunner A / Milligan RA / Potter CS / Carragher B / Williamson JR
CitationJournal: Science / Year: 2010
Title: Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit.
Authors: Anke M Mulder / Craig Yoshioka / Andrea H Beck / Anne E Bunner / Ronald A Milligan / Clinton S Potter / Bridget Carragher / James R Williamson
DateDeposition: Sep 11, 2013 / Header (metadata) release: Sep 25, 2013 / Map release: Sep 25, 2013 / Last update: Dec 11, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2453.map.gz (map file in CCP4 format, 105470 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.63 Å/pix.
= 489. Å
300 pix
1.63 Å/pix.
= 489. Å
300 pix
1.63 Å/pix.
= 489. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density
Contour Level:0.9 (by author), 0.9 (movie #1):
Minimum - Maximum-1.53980339 - 3.59133363
Average (Standard dev.)-0.07092217 (0.19621447)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
CellA=B=C: 489.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z489.000489.000489.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-1.5403.591-0.071

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Supplemental data

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Sample components

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Entire 30S Reconstitution Reaction

EntireName: 30S Reconstitution Reaction / Number of components: 1
MassTheoretical: 789 kDa

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Component #1: ribosome-prokaryote, 30S Ribosome Subunit

Ribosome-prokaryoteName: 30S Ribosome Subunit / a.k.a: 30S Subunit / Prokaryote: SSU 30S, PSR16s / Recombinant expression: No
MassTheoretical: 789 kDa
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jan 7, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Single tilt / Model: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 6635

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4739
3D reconstructionAlgorithm: Random conical tilt / Software: Appion, Spider, Eman / CTF correction: Ace2 / Resolution: 31.67 Å / Resolution method: FSC 0.5

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