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- EMDB-1895: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1895
TitleCryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor
Map dataYjeQ in complex with the 30S ribosomal subunit
Sample
  • Sample: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
  • Complex: 30S ribosomal subunitProkaryotic small ribosomal subunit
  • Protein or peptide: RsgA, YjeQ
KeywordsRibosome assembly / 30S subunit / YjeQ protein / RsgA protein / GTPase
Function / homology
Function and homology information


mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / regulation of DNA-templated transcription elongation / transcription antitermination / maintenance of translational fidelity / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / tRNA binding / molecular adaptor activity / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily ...Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S2, conserved site / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, N-terminal domain
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S17 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 30S ribosomal protein S14 / 30S ribosomal protein S15 / 30S ribosomal protein S17 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.5 Å
AuthorsJomaa A / Stewart G / Mears JA / Kireeva I / Brown ED / Ortega J
CitationJournal: RNA / Year: 2011
Title: Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor.
Authors: Ahmad Jomaa / Geordie Stewart / Jason A Mears / Inga Kireeva / Eric D Brown / Joaquin Ortega /
Abstract: YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ ...YjeQ is a protein broadly conserved in bacteria containing an N-terminal oligonucleotide/oligosaccharide fold (OB-fold) domain, a central GTPase domain, and a C-terminal zinc-finger domain. YjeQ binds tightly and stoichiometrically to the 30S subunit, which stimulates its GTPase activity by 160-fold. Despite growing evidence for the involvement of the YjeQ protein in bacterial 30S subunit assembly, the specific function and mechanism of this protein remain unclear. Here, we report the costructure of YjeQ with the 30S subunit obtained by cryo-electron microscopy. The costructure revealed that YjeQ interacts simultaneously with helix 44, the head and the platform of the 30S subunit. This binding location of YjeQ in the 30S subunit suggests a chaperone role in processing of the 3' end of the rRNA as well as in mediating the correct orientation of the main domains of the 30S subunit. In addition, the YjeQ binding site partially overlaps with the interaction site of initiation factors 2 and 3, and upon binding, YjeQ covers three inter-subunit bridges that are important for the association of the 30S and 50S subunits. Hence, our structure suggests that YjeQ may assist in ribosome maturation by preventing premature formation of the translation initiation complex and association with the 50S subunit. Together, these results support a role for YjeQ in the late stages of 30S maturation.
History
DepositionApr 18, 2011-
Header (metadata) releaseMay 27, 2011-
Map releaseOct 28, 2011-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0088
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0088
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4a2i
  • Surface level: 0.0088
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

YjeQ+30S.tif

Downloads & links

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Map

FileDownload / File: emd_1895.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYjeQ in complex with the 30S ribosomal subunit
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour LevelBy AUTHOR: 0.0088 / Movie #1: 0.0088
Minimum - Maximum-0.0217409 - 0.0623605
Average (Standard dev.)0.000295723 (±0.00440148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 325.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z325.120325.120325.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0220.0620.000

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Supplemental data

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Sample components

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Entire : Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...

EntireName: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
Components
  • Sample: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
  • Complex: 30S ribosomal subunitProkaryotic small ribosomal subunit
  • Protein or peptide: RsgA, YjeQ

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Supramolecule #1000: Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...

SupramoleculeName: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein
type: sample / ID: 1000 / Details: 30S was mixed with YjeQ in 1-to-5 molar ratio / Number unique components: 2
Molecular weightTheoretical: 900 KDa

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Supramolecule #1: 30S ribosomal subunit

SupramoleculeName: 30S ribosomal subunit / type: complex / ID: 1 / Name.synonym: 30S subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 900 KDa

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Macromolecule #1: RsgA, YjeQ

MacromoleculeName: RsgA, YjeQ / type: protein_or_peptide / ID: 1 / Name.synonym: Assembly factor / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113 / Cell: Cytoplasm
Molecular weightExperimental: 39 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pDEST17-YjeQ

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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

Concentration0.9 mg/mL
BufferpH: 7.5
Details: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol.
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: FEI Vitrobot III / Method: Blot for 7 seconds

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.0 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.65 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from -175 C to ambient
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Corrected at 200000 times magnification
DateMay 12, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 2.54 µm / Number real images: 150 / Average electron dose: 15 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 16228
DetailsParticles were picked with Boxer.

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Atomic model buiding 1

Initial modelPDB ID:

2avy
PDB Unreleased entry

SoftwareName: Chimera
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor
Output model

PDB-4a2i:
Cryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor

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Atomic model buiding 2

Initial modelPDB ID:

2rcn

SoftwareName: Chimera
DetailsProtocol: Rigid Body. Each domain of YjeQ was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor
Output model

PDB-4a2i:
Cryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor

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