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- EMDB-1413: Structural aspects of RbfA action during small ribosomal subunit ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1413
TitleStructural aspects of RbfA action during small ribosomal subunit assembly.
Map dataCryo-EM map of Thermus thermophilus 30S subunit and RbfA complex.
Sample
  • Sample: Complex of ribosomal subunit 30S and RbfA
  • Complex: 30S small ribosomal subunit
  • Protein or peptide: Ribosome binding factor A
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / cytosol
Similarity search - Function
Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal ...Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / K homology domain-like, alpha/beta / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S12 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Ribosome-binding factor A
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsDatta PP / Wilson DN / Kawazoe M / Swami NK / Kaminishi T / Sharma MR / Booth TM / Takemoto C / Fucini P / Yokoyama S / Agrawal RK
CitationJournal: MOLECULAR CELL / Year: 2007
Title: Structural aspects of RbfA action during small ribosomal subunit assembly.
Authors: Datta PP / Wilson DN / Kawazoe M / Swami NK / Kaminishi T / Sharma MR / Booth TM / Takemoto C / Fucini P / Yokoyama S / Agrawal RK
History
DepositionAug 20, 2007-
Header (metadata) releaseAug 21, 2007-
Map releaseNov 16, 2007-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2r1c, PDB-2r1g
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2r1c
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2r1g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_1413.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Thermus thermophilus 30S subunit and RbfA complex.
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour Level1: 36.700000000000003 / Movie #1: 35
Minimum - Maximum-130.322000000000003 - 407.386000000000024
Average (Standard dev.)2.66509 (±22.7014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 358.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z358.800358.800358.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-90
NX/NY/NZ181181181
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-130.322407.3862.665

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Supplemental data

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Sample components

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Entire : Complex of ribosomal subunit 30S and RbfA

EntireName: Complex of ribosomal subunit 30S and RbfA
Components
  • Sample: Complex of ribosomal subunit 30S and RbfA
  • Complex: 30S small ribosomal subunit
  • Protein or peptide: Ribosome binding factor A

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Supramolecule #1000: Complex of ribosomal subunit 30S and RbfA

SupramoleculeName: Complex of ribosomal subunit 30S and RbfA / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 910.9 KDa

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Supramolecule #1: 30S small ribosomal subunit

SupramoleculeName: 30S small ribosomal subunit / type: complex / ID: 1 / Name.synonym: 30S / Details: Thermus thermophilus / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightExperimental: 900 KDa

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Macromolecule #1: Ribosome binding factor A

MacromoleculeName: Ribosome binding factor A / type: protein_or_peptide / ID: 1 / Name.synonym: RbfA / Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Molecular weightExperimental: 10.9 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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: 7.8
Details: 20mM Hepes-KOH (pH7.8), 10mM Mg(OAc)2, 200 mM NH4Cl, 65 mM KCL.
GridDetails: Quantifoil 300 mesh Copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Wadworth Center own cryo-plunger fabricated on-site
Method: 5ul of specimen was applied to the grid, then blotted using Whatman number 1 filter paper for 2 to 4 seconds, then plunged.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: Objective lends astigmatism corrected at 210x magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 131 / Average electron dose: 20 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Oxford cryo-transfer holder / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 61207

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Atomic model buiding 1

SoftwareName: O
DetailsProtocol: Rigid Body. The domains were fitted independently using the program O
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2r1c:
Coordinates of the thermus thermophilus ribosome binding factor A (RbfA) homology model as fitted into the CRYO-EM map of a 30S-RBFA complex

PDB-2r1g:
Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex

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