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Yorodumi- EMDB-1895: Cryo-electron Microscopy Structure of the 30S Subunit in Complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1895 | |||||||||
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Title | Cryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor | |||||||||
Map data | YjeQ in complex with the 30S ribosomal subunit | |||||||||
Sample |
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Keywords | Ribosome assembly / 30S subunit / YjeQ protein / RsgA protein / GTPase | |||||||||
Function / homology | Function and homology information ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded 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 ...ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / misfolded 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 / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.5 Å | |||||||||
Authors | Jomaa A / Stewart G / Mears JA / Kireeva I / Brown ED / Ortega J | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1895.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-1895-v30.xml emd-1895.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | YjeQ+30S.tif | 136.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1895 | HTTPS FTP |
-Validation report
Summary document | emd_1895_validation.pdf.gz | 230.8 KB | Display | EMDB validaton report |
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Full document | emd_1895_full_validation.pdf.gz | 229.9 KB | Display | |
Data in XML | emd_1895_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1895 | HTTPS FTP |
-Related structure data
Related structure data | 4a2iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1895.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | YjeQ in complex with the 30S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...
Entire | Name: Escherichia coli 30S ribosomal subunit in complex with the YjeQ protein |
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Components |
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-Supramolecule #1000: Escherichia coli 30S ribosomal subunit in complex with the YjeQ p...
Supramolecule | Name: 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 |
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Molecular weight | Theoretical: 900 KDa |
-Supramolecule #1: 30S ribosomal subunit
Supramolecule | Name: 30S ribosomal subunit / type: complex / ID: 1 / Name.synonym: 30S subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 900 KDa |
-Macromolecule #1: RsgA, YjeQ
Macromolecule | Name: RsgA, YjeQ / type: protein_or_peptide / ID: 1 / Name.synonym: Assembly factor / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: BW25113 / Cell: Cytoplasm |
Molecular weight | Experimental: 39 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pDEST17-YjeQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM Tris-HCl pH 7.5, 10 mM magnesium acetate, 60 mM NH4Cl, 3 mM 2-mercaptoethanol. |
Grid | Details: 200 mesh copper grid |
Vitrification | Cryogen 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 |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 200000 times magnification |
Date | May 12, 2010 |
Image recording | Category: 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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.65 µm / Nominal magnification: 50000 |
Sample stage | Specimen 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 |
-Image processing
Details | Particles were picked with Boxer. |
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CTF correction | Details: Each micrograph |
Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: 2avy |
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Software | Name: Chimera |
Details | Protocol: Rigid Body. Each domain of YjeQ was fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor |
Output model | PDB-4a2i: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: Rigid Body. Each domain of YjeQ was fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor |
Output model | PDB-4a2i: |