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- EMDB-2455: 30S Ribosome Subunit Assembly Intermediates, Intermediate 4c -

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Basic information

Entry
Database: EMDB / ID: EMD-2455
Title30S Ribosome Subunit Assembly Intermediates, Intermediate 4c
Map dataAssembly Intermediate Group 4c
Sample
  • Sample: 30S Reconstitution Reaction
  • Complex: 30S Ribosome Subunit
KeywordsRibosome Assembly / 30S Ribosome Subunit / 30S Assembly / Time-resolved electron microscopy / Discovery Single-particle Profiling / 30S Ribosome Subunit Assembly Intermediate
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 47.07 Å
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 /
Abstract: Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the ...Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.
History
DepositionSep 11, 2013-
Header (metadata) releaseSep 25, 2013-
Map releaseSep 25, 2013-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2455grp4...

Downloads & links

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Map

FileDownload / File: emd_2455.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAssembly Intermediate Group 4c
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.55 Å/pix.
x 300 pix.
= 465. Å		1.55 Å/pix.
x 300 pix.
= 465. Å		1.55 Å/pix.
x 300 pix.
= 465. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-1.72492301 - 4.02784777
Average (Standard dev.)-0.07152414 (±0.2056841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 465.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.551.551.55
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z465.000465.000465.000
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-1.7254.028-0.072

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Supplemental data

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Sample components

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Entire : 30S Reconstitution Reaction

EntireName: 30S Reconstitution Reaction
Components
  • Sample: 30S Reconstitution Reaction
  • Complex: 30S Ribosome Subunit

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Supramolecule #1000: 30S Reconstitution Reaction

SupramoleculeName: 30S Reconstitution Reaction / type: sample / ID: 1000 / Number unique components: 21
Molecular weightTheoretical: 789 KDa

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Supramolecule #1: 30S Ribosome Subunit

SupramoleculeName: 30S Ribosome Subunit / type: complex / ID: 1 / Name.synonym: 30S Subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S, PSR16s
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 789 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 25 mM Tris-HCl, 330 mM KCl, 20 mM MgCl2, 2 mM DTT
StainingType: NEGATIVE / Details: 2% UA
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 7, 2009
Image recordingNumber real images: 6635
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Single tilt / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Ace2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 47.07 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Appion, Spider, Eman / Number images used: 1612

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