+Open data
-Basic information
Entry | Database: PDB / ID: 7afq | |||||||||
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Title | Ribosome binding factor A (RbfA) | |||||||||
Components | Ribosome-binding factor A | |||||||||
Keywords | RNA BINDING PROTEIN / Solution state NMR / 30S biogenesis / ribosome assembly / RbfA. | |||||||||
Function / homology | Function and homology information ribosomal small subunit binding / maturation of SSU-rRNA / response to cold / ribosomal small subunit biogenesis / ribosome biogenesis / DNA damage response / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli O26:H11 (bacteria) | |||||||||
Method | SOLUTION NMR / simulated annealing / molecular dynamics | |||||||||
Authors | Schedlbauer, A. / Iturrioz, I. / Ochoa-Lizarralde, B. / Diercks, T. / Fucini, P. / Connell, S. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Sci Adv / Year: 2021 Title: A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de ...Authors: Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell / Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7afq.cif.gz | 581 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7afq.ent.gz | 491.6 KB | Display | PDB format |
PDBx/mmJSON format | 7afq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/7afq ftp://data.pdbj.org/pub/pdb/validation_reports/af/7afq | HTTPS FTP |
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-Related structure data
Related structure data | 7af3C 7af5C 7af8C 7afaC 7afdC 7afhC 7afiC 7afkC 7aflC 7afnC 7afoC 7afrC 7bodC 7boeC 7bofC 7bogC 7bohC 7boiC 7narC 7nasC 7natC 7nauC 7navC 7naxC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15176.503 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O26:H11 (bacteria) / Gene: rbfA, B9S25_002975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B7PAU8, UniProt: P0A7G2*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 400 uM [U-13C; U-15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP, 90% H2O/10% D2O Label: sample 1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 40 mM / Label: condition_1 / pH: 7.6 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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