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- EMDB-8626: Structure of the 30S subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-8626
TitleStructure of the 30S subunit
Map data
Sample30S Consensus subunit
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination ...guanosine tetraphosphate binding / Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides / mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit biogenesis / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / positive regulation of translational fidelity / endodeoxyribonuclease activity / maintenance of translational fidelity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / small ribosomal subunit / GDP binding / cytosolic small ribosomal subunit / regulation of translation / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / response to antibiotic / GTP binding / zinc ion binding / membrane / metal ion binding / cytosol
Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / Ribosome biogenesis GTPase RsgA / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S19/S15 ...Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S20 / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / Ribosome biogenesis GTPase RsgA / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S19/S15 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S5 / Ribosomal protein S18, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5, N-terminal / Ribosomal protein S5, bacterial-type / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S14, conserved site / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S6 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S8 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S19 conserved site / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S3, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6, conserved site / Ribosomal protein S13, conserved site
30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S5 ...30S ribosomal protein S2 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / Small ribosomal subunit biogenesis GTPase RsgA / 30S ribosomal protein S3 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 30S ribosomal protein S5 / 30S ribosomal protein S15 / 30S ribosomal protein S14 / 30S ribosomal protein S10 / 30S ribosomal protein S13 / 30S ribosomal protein S19 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / 30S ribosomal protein S16 / 30S ribosomal protein S12 / 30S ribosomal protein S10 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S9 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S15
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsRazi A / Guarne A / Ortega J
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Authors: Aida Razi / Alba Guarné / Joaquin Ortega /
Abstract: Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with ...Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.
History
DepositionFeb 26, 2017-
Header (metadata) releaseMar 15, 2017-
Map releaseApr 19, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0215
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0215
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8626.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 220 pix.
= 319. Å
1.45 Å/pix.
x 220 pix.
= 319. Å
1.45 Å/pix.
x 220 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.0215 / Movie #1: 0.0215
Minimum - Maximum-0.031991478 - 0.10743945
Average (Standard dev.)0.0010633138 (±0.0056903656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0320.1070.001

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Supplemental data

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Sample components

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Entire 30S Consensus subunit

EntireName: 30S Consensus subunit / Number of components: 1

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Component #1: protein, 30S Consensus subunit

ProteinName: 30S Consensus subunit / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 10 mM Tris-HCl at pH 7.5, 10 mM magnesium acetate, 150 mM NH4Cl, 3mM 2-mercaptoethanol and 2 mM GMP-PNP
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000. X (nominal), 34482. X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 142945
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body

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