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- EMDB-2019: Structure of the E. coli 30S ribosomal subunit from a ksgA deleti... -

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Basic information

Entry
Database: EMDB / ID: EMD-2019
TitleStructure of the E. coli 30S ribosomal subunit from a ksgA deletion strain
Map dataE. coli 30S ribosomal subunit from a ksgA deletion strain
Sample
  • Sample: E. coli 30S ribosomal subunit from a ksgA deletion strain
  • Complex: 30S ribosomal subunit
Keywordsribosome biogenesis / methyltransferase / KsgA / small ribosomal subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.5 Å
AuthorsBoehringer D / O'Farrell HC / Rife JP / Ban N
CitationJournal: J Biol Chem / Year: 2012
Title: Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis.
Authors: Daniel Boehringer / Heather C O'Farrell / Jason P Rife / Nenad Ban /
Abstract: The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal ...The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.
History
DepositionJan 3, 2012-
Header (metadata) releaseJan 20, 2012-
Map releaseFeb 15, 2012-
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: 38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 38
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2019.jpg

Downloads & links

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Map

FileDownload / File: emd_2019.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli 30S ribosomal subunit from a ksgA deletion strain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.09 Å/pix.
x 96 pix.
= 392.64 Å		4.09 Å/pix.
x 96 pix.
= 392.64 Å		4.09 Å/pix.
x 96 pix.
= 392.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 38.0 / Movie #1: 38
Minimum - Maximum-204.322448729999991 - 359.860809329999995
Average (Standard dev.)-16.871873860000001 (±22.594120029999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-48-48-48
Dimensions969696
Spacing969696
CellA=B=C: 392.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.094.094.09
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z392.640392.640392.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-48-48-48
NC/NR/NS969696
D min/max/mean-204.322359.861-16.872

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Supplemental data

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Sample components

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Entire : E. coli 30S ribosomal subunit from a ksgA deletion strain

EntireName: E. coli 30S ribosomal subunit from a ksgA deletion strain
Components
  • Sample: E. coli 30S ribosomal subunit from a ksgA deletion strain
  • Complex: 30S ribosomal subunit

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Supramolecule #1000: E. coli 30S ribosomal subunit from a ksgA deletion strain

SupramoleculeName: E. coli 30S ribosomal subunit from a ksgA deletion strain
type: sample / ID: 1000
Details: 30S ribosomal subunits lack the methylations at A1518 and A1519
Oligomeric state: One ribosomal small subunit / Number unique components: 1
Molecular weightExperimental: 790 KDa / Theoretical: 790 KDa

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Supramolecule #1: 30S ribosomal subunit

SupramoleculeName: 30S ribosomal subunit / type: complex / ID: 1 / Name.synonym: small ribosomal subunit
Details: 30S ribosomal subunits lack the methylation at A1518 and A1519
Recombinant expression: Yes / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 790 KDa / Theoretical: 790 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: 7.6
Details: 100 mM NH4Cl, 4 mM MgCl2, 20 mM HEPES/KOH pH 7.6, 3 mM DTT
GridDetails: Quantifoil 200 mesh copper
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger

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Electron microscopy

MicroscopeFEI TECNAI 20
DetailsSemi-automatic data acquisition with SerialEM script
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 82000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Per image, ctffind3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic-5, Spider / Number images used: 39846

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