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- EMDB-21572: 30S-Inactive-low-Mg2+ Class A -

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Basic information

Entry
Database: EMDB / ID: EMD-21572
Title30S-Inactive-low-Mg2+ Class A
Map data
Sample30S-Activated-high-Mg2+:
nucleic-acidNucleic acid / (30S ribosomal protein ...) x 14
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 / maintenance of translational fidelity / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / 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
Ribosomal protein S4, bacterial-type / K Homology domain / Ribosomal protein S5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein S3, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain, type 2 / Ribosomal protein S12/S23 ...Ribosomal protein S4, bacterial-type / K Homology domain / Ribosomal protein S5, bacterial-type / Ribosomal protein S19 conserved site / Ribosomal protein S3, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S15, bacterial-type / K Homology domain, type 2 / Ribosomal protein S12/S23 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S19, bacterial-type / K homology domain superfamily, prokaryotic type / Ribosomal protein S14 / Ribosomal protein S13, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / S15/NS1, RNA-binding / Ribosomal protein S5, N-terminal, 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 / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / Ribosomal protein S3, C-terminal / Ribosomal protein S5 / Ribosomal protein S16, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S14/S29 / RNA-binding S4 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S9 / Ribosomal protein S19, superfamily / Ribosomal protein S9, conserved site / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S16 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S17/S11
30S ribosomal protein S4 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S15 / 30S ribosomal protein S3 / 30S ribosomal protein S20 / 30S ribosomal protein S19 ...30S ribosomal protein S4 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S15 / 30S ribosomal protein S3 / 30S ribosomal protein S20 / 30S ribosomal protein S19 / 30S ribosomal protein S16 / 30S ribosomal protein S13 / 30S ribosomal protein S12 / 30S ribosomal protein S10 / 30S ribosomal protein S17
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJahagirdar D / Jha V / Basu B / Gomez-Blanco J / Vargas J / Ortega 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) releaseOct 21, 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: 4.43
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 4.43
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w7n
  • Surface level: 4.43
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21572.png

Downloads & links

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Map

FileDownload / File: emd_21572.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.43 / Movie #1: 4.43
Minimum - Maximum-19.302412 - 36.617325
Average (Standard dev.)-0.00000000001 (±0.9919078)
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/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-19.30236.617-0.000

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Supplemental data

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Sample components

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Entire 30S-Activated-high-Mg2+

EntireName: 30S-Activated-high-Mg2+ / Number of components: 16

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Component #1: protein, 30S-Activated-high-Mg2+

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

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Component #2: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCGUGCCA GCAGCCGCGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAUGCAAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUGGCCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC GCCCGUCACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCGUAA CAAGGUAACC GUAGGGGAAC CUGCGGUUGG AUCACCUCCU UA
MassTheoretical: 499.690031 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #6: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #7: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #8: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #9: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.768157 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #10: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #11: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #12: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.319882 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #13: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #14: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #15: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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Component #16: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12

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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: 421738
3D reconstructionSoftware: RELION / Resolution: 3.4 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

4v4q

Output model

6w7n

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