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- EMDB-5598: Structure of the immature 30S subunit from a Escherichia coli rim... -

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Basic information

Entry
Database: EMDB / ID: EMD-5598
TitleStructure of the immature 30S subunit from a Escherichia coli rimM null strain. Conformation 4.
Map dataStructure of the immature 30S subunit from a Escherichia coli rimM null strain. Conformation 4.
Sample
  • Sample: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 4
  • Complex: ribosome 30S subunit
KeywordsRibosome assembly / 30S subunit / RimM protein
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsLeong V / Kent M / Jomaa A / Ortega J
CitationJournal: RNA / Year: 2013
Title: Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement.
Authors: Vivian Leong / Meredith Kent / Ahmad Jomaa / Joaquin Ortega /
Abstract: Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of ...Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of the maturation process of the small subunit. However, it is unclear how the functional interplay between these factors occurs in the context of multiple parallel pathways. To understand how these factors work together, we have characterized the immature 30S subunits that accumulate in ΔrimM cells and compared them with immature 30S subunits from a ΔyjeQ strain. The cryo-EM maps obtained from these particles showed that the densities representing helices 44 and 45 in the rRNA were partially missing, suggesting mobility of these motifs. These 30S subunits were also partially depleted in all tertiary ribosomal proteins, particularly those binding in the head domain. Using image classification, we identified four subpopulations of ΔrimM immature 30S subunits differing in the amount of missing density for helices 44 and 45, as well as the amount of density existing in these maps for the underrepresented proteins. The structural defects found in these immature subunits resembled those of the 30S subunits that accumulate in the ΔyjeQ strain. These findings are consistent with an "early convergency model" in which multiple parallel assembly pathways of the 30S subunit converge into a late assembly intermediate, as opposed to the mature state. Functionally related factors will bind to this intermediate to catalyze the last steps of maturation leading to the mature 30S subunit.
History
DepositionMar 6, 2013-
Header (metadata) releaseMar 20, 2013-
Map releaseMay 8, 2013-
UpdateMay 29, 2013-
Current statusMay 29, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5598.tif

Downloads & links

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Map

FileDownload / File: emd_5598.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the immature 30S subunit from a Escherichia coli rimM null strain. Conformation 4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 128 pix.
= 256. Å		2 Å/pix.
x 128 pix.
= 256. Å		2 Å/pix.
x 128 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.222
CCP4 map header222
EM Navigator Movie #12.542.542.54
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.03942204 - 14.74941254
Average (Standard dev.)0.0 (±0.98962915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-5.03914.7490.000

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Supplemental data

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Sample components

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Entire : Structure of an immature 30S subunit from an E. coli rimM null st...

EntireName: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 4
Components
  • Sample: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 4
  • Complex: ribosome 30S subunit

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Supramolecule #1000: Structure of an immature 30S subunit from an E. coli rimM null st...

SupramoleculeName: Structure of an immature 30S subunit from an E. coli rimM null strain. Conformation 4
type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 930 KDa / Theoretical: 930 KDa

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Supramolecule #1: ribosome 30S subunit

SupramoleculeName: ribosome 30S subunit / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: SSU 30S, PSR16s
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113 / Location in cell: cytoplasm
Molecular weightExperimental: 930 KDa / Theoretical: 930 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 10 mM Tris-HCl, pH 7.5, 10 mM Mg acetate, 60 mM NH4Cl and 3 mM 2-mercaptoethanol
GridDetails: 400 mesh cupped grid with thin carbon support, glow discharged in air
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III / Method: Blot twice for 7 seconds each.

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 97 K
DateJul 10, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 250 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsReconstruction obtained with Xmipp
CTF correctionDetails: CTFFIND
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 23275

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