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- EMDB-21570: 30S-Inactive-high-Mg2+ Class B -

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Basic information

Entry
Database: EMDB / ID: EMD-21570
Title30S-Inactive-high-Mg2+ Class B
Map data
Sample30S-Inactive-high-Mg2+ Class B
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity, mRNA regulatory element binding / endodeoxyribonuclease activity / positive regulation of RNA splicing / DNA-templated transcription, termination / positive regulation of translational fidelity / maintenance of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / cytosolic small ribosomal subunit / regulation of translation / regulation of mRNA stability / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / RNA binding / cytosol
K homology domain superfamily, prokaryotic type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S12, bacterial-type ...K homology domain superfamily, prokaryotic type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Nucleic acid-binding, OB-fold / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S13 / Ribosomal protein S17, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S10 / Ribosomal protein S4/S9 / Ribosomal protein S16 domain superfamily / Ribosomal protein S14/S29 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S18 / Ribosomal protein S19 conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S17/S11 / Ribosomal protein S3, C-terminal / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein S6 / Ribosomal protein S14, bacterial/plastid
30S ribosomal protein S3 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S10 / 30S ribosomal protein S20 / 30S ribosomal protein S19 ...30S ribosomal protein S3 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S10 / 30S ribosomal protein S20 / 30S ribosomal protein S19 / 30S ribosomal protein S18 / 30S ribosomal protein S16 / 30S ribosomal protein S13 / 30S ribosomal protein S12 / 30S ribosomal protein S11 / 30S ribosomal protein S6 / 30S ribosomal protein S17
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsOrtega J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR PJT- 153044 Canada
CitationJournal: RNA / Year: 2020
Title: Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.
Authors: Dushyant Jahagirdar / Vikash Jha / Kaustuv Basu / Josue Gomez-Blanco / Javier Vargas / Joaquin Ortega /
Abstract: It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits ...It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an "active" and "inactive" conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains unsolved. Here we used cryo-electron microscopy to obtain the structure of the inactive conformation of the 30S subunit to 3.6 Å resolution and study its motions. In the inactive conformation, an alternative base-pairing of three nucleotides causes the region of helix 44, forming the decoding center to adopt an unlatched conformation and the 3' end of the 16S rRNA positions similarly to the mRNA during translation. Incubation of inactive 30S subunits at 42°C reverts these structural changes. The air-water interface to which ribosome subunits are exposed during sample preparation also peel off some ribosomal proteins. Extended exposures to low magnesium concentrations make the ribosomal particles more susceptible to the air-water interface causing the unfolding of large rRNA structural domains. Overall, this study provides new insights about the conformational space explored by the 30S ribosomal subunit when the ribosomal particles are free in solution.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 19, 2020-
Header (metadata) releaseApr 1, 2020-
Map releaseOct 21, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0374
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0374
  • 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_21570.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 304 pix.
= 326.192 Å
1.07 Å/pix.
x 304 pix.
= 326.192 Å
1.07 Å/pix.
x 304 pix.
= 326.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 0.0374 / Movie #1: 0.0374
Minimum - Maximum-0.07359244 - 0.16382356
Average (Standard dev.)0.0009821714 (±0.006700625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 326.192 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z326.192326.192326.192
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0740.1640.001

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Supplemental data

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Sample components

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Entire 30S-Inactive-high-Mg2+ Class B

EntireName: 30S-Inactive-high-Mg2+ Class B / Number of components: 1

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Component #1: protein, 30S-Inactive-high-Mg2+ Class B

ProteinName: 30S-Inactive-high-Mg2+ Class B / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 52 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 118725
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4V4Q

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