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- EMDB-0482: Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit -

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Entry
Database: EMDB / ID: EMD-0482
TitleRole of Era in Assembly and Homeostasis of the Ribosomal Small Subunit
Map data
Sample30S assembly intermediate (class P):
(30S ribosomal protein ...) x 15 / nucleic-acidNucleic acid / ligand
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding
Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily ...Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S2 signature 1. / Ribosomal protein S10 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S19 / Ribosomal protein S15 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S8 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / KH domain / Ribosomal protein S2 / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S16 / Ribosomal protein S8 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S6, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S14 / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S8 / K Homology domain, type 2 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S2 signature 2. / Ribosomal protein S6 signature. / Type-2 KH domain profile. / S4 RNA-binding domain profile. / RNA-binding S4 domain / K Homology domain / 30S ribosomal protein S17 / Ribosomal protein S15, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Translation elongation factor EF1B/ribosomal protein S6 / Nucleic acid-binding, OB-fold / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Ribosomal protein S12/S23 / Ribosomal protein S19, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S4 signature.
30S ribosomal protein S19 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S16 / 30S ribosomal protein S15 / 30S ribosomal protein S4 / 30S ribosomal protein S10 / 30S ribosomal protein S8 / 30S ribosomal protein S18 / 30S ribosomal protein S3 ...30S ribosomal protein S19 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S16 / 30S ribosomal protein S15 / 30S ribosomal protein S4 / 30S ribosomal protein S10 / 30S ribosomal protein S8 / 30S ribosomal protein S18 / 30S ribosomal protein S3 / un:a0a0t5xim4: / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S6 / 30S ribosomal protein S12
Biological speciesEscherichia coli (E. coli) / Escherichia coli H736 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOrtega J
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Role of Era in assembly and homeostasis of the ribosomal small subunit.
Authors: Aida Razi / Joseph H Davis / Yumeng Hao / Dushyant Jahagirdar / Brett Thurlow / Kaustuv Basu / Nikhil Jain / Josue Gomez-Blanco / Robert A Britton / Javier Vargas / Alba Guarné / Sarah A Woodson / James R Williamson / Joaquin Ortega /
Abstract: Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is ...Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.
Validation ReportPDB-ID: 6nqb

SummaryFull reportAbout validation report
DateDeposition: Jan 20, 2019 / Header (metadata) release: May 22, 2019 / Map release: Jun 26, 2019 / Update: Jul 17, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 5.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nqb
  • Surface level: 5.18
  • 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_0482.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
AxesX (Sec.)Y (Row.)Z (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: 5.18 / Movie #1: 5.18
Minimum - Maximum-13.176378 - 32.912869999999998
Average (Standard dev.)0.000000000002664 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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/S321
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-13.17632.9130.000

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Supplemental data

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Sample components

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Entire 30S assembly intermediate (class P)

EntireName: 30S assembly intermediate (class P)
Details: 30S assembly intermediate (class P) purified from Era-depleted E.coli cells
Number of components: 18

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Component #1: protein, 30S assembly intermediate (class P)

ProteinName: 30S assembly intermediate (class P)
Details: 30S assembly intermediate (class P) purified from Era-depleted E.coli cells
Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K-12

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Component #2: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.078785 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.196988 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.360276 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.441836 kDa
SourceSpecies: Escherichia coli H736 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: nucleic-acid, 16S RIBOSOMAL RNA

nucleic acidName: 16S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
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 (E. coli)

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Component #7: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.383002 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.675102 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.972643 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.015361 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.636961 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.944415 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, 30S RIBOSOMAL PROTEIN bS16

ProteinName: 30S RIBOSOMAL PROTEIN bS16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.936237 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.164815 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.109118 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #16: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.50619 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #17: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.12275 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
Support film5 mA
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298.15 K / Humidity: 100 %

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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: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250.0 - 2750.0 nm
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: 423567
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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