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Yorodumi- PDB-4adv: Structure of the E. coli methyltransferase KsgA bound to the E. c... -
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-Basic information
Entry | Database: PDB / ID: 4adv | ||||||
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Title | Structure of the E. coli methyltransferase KsgA bound to the E. coli 30S ribosomal subunit | ||||||
Components |
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Keywords | TRANSLATION / RIBOSOME BIOGENESIS / SMALL RIBOSOMAL SUBUNIT | ||||||
Function / homology | Function and homology information 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / ribosomal small subunit binding / 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 / DNA endonuclease activity / regulation of DNA-templated transcription elongation / maturation of SSU-rRNA / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / rRNA processing / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / double-stranded DNA binding / cytosolic small ribosomal subunit / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å | ||||||
Authors | Boehringer, D. / O'Farrell, H.C. / Rife, J.P. / Ban, N. | ||||||
Citation | Journal: J Biol Chem / Year: 2012 Title: Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. Authors: Daniel Boehringer / Heather C O'Farrell / Jason P Rife / Nenad Ban / Abstract: The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal ...The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 4adv.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4adv.ent.gz | 901.2 KB | Display | PDB format |
PDBx/mmJSON format | 4adv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4adv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4adv_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4adv_validation.xml.gz | 131.3 KB | Display | |
Data in CIF | 4adv_validation.cif.gz | 202.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adv ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adv | HTTPS FTP |
-Related structure data
Related structure data | 2017MC 2019C 2020C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU
#2: Protein | Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V0 |
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#3: Protein | Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V3 |
#4: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7V8 |
#5: Protein | Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7W1 |
#6: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02358 |
#7: Protein | Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02359 |
#8: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7W7 |
#9: Protein | Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7X3 |
#10: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7R5 |
#11: Protein | Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7R9 |
#12: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7S3 |
#13: Protein | Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7S9 |
#14: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02370, UniProt: P0AG59*PLUS |
#15: Protein | Mass: 10319.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02371, UniProt: P0ADZ4*PLUS |
#16: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7T3 |
#17: Protein | Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P02373, UniProt: P0AG63*PLUS |
#18: Protein | Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7T7 |
#19: Protein | Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7U3 |
#20: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P0A7U7 |
#21: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: UniProt: P68679 |
-RNA chain / Protein / Non-polymers , 3 types, 141 molecules AV
#1: RNA chain | Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: KASUGAMYCIN RESISTANT / Strain: MRE600 / References: GenBank: 33357879 |
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#22: Protein | Mass: 27988.273 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HMS174 References: UniProt: P06992, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase |
#23: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. COLI METHYLTRANSFERASE KSGA BOUND TO THE E. COLI 30S RIBOSOMAL SUBUNIT Type: COMPLEX |
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Buffer solution | Name: 40 MM KCL, 4MM MGCL2, 20 MM HEPES/KOH PH 7. 6, 6 MM 2- MERCAPTOETHANOL pH: 7.6 Details: 40 MM KCL, 4MM MGCL2, 20 MM HEPES/KOH PH 7. 6, 6 MM 2- MERCAPTOETHANOL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- PLUNGER, |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 Details: SEMI-AUTOMATIC DATA ACQUISITION WITH SERIAL EM SCRIPT |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 62000 X / Calibrated magnification: 82000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: PER IMAGE, CTFFIND3 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: ANGULAR RECONSTITUTION, PROJECTION MATCHING / Resolution: 13.5 Å / Num. of particles: 23343 / Actual pixel size: 3.07 Å Details: 30S RIBOSOMAL SUBUNIT HEAD AND BODY WERE FITTED SEPARATELY AS RIGID BODIES. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2017. (DEPOSITION ID: 10519). Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--XRAY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 13.5 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 13.5 Å
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