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Yorodumi- PDB-9ax8: 70S initiation complex (tRNA-fMet M1, initiation factor 2 + CUG s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ax8 | ||||||||||||||||||
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Title | 70S initiation complex (tRNA-fMet M1, initiation factor 2 + CUG start codon) | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / translation initiation / tRNA-fMet M1 / frameshifting / initiation factor 2 | ||||||||||||||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / translation initiation factor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal small subunit biogenesis ...guanosine tetraphosphate binding / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / translation initiation factor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||||||||
Authors | Mattingly, J.M. / Nguyen, H.A. / Dunham, C.M. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: J Biol Chem / Year: 2024 Title: Structural analysis of noncanonical translation initiation complexes. Authors: Jacob M Mattingly / Ha An Nguyen / Bappaditya Roy / Kurt Fredrick / Christine M Dunham / Abstract: Translation initiation is a highly regulated, multi-step process which is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a ...Translation initiation is a highly regulated, multi-step process which is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a dedicated initiator fMet-tRNA bind the small (30S) ribosomal subunit. Specific binding of fMet-tRNA in the peptidyl (P) site is mediated by the inspection of the fMet moiety by initiation factor IF2 and of three conserved G-C base pairs in the tRNA anticodon stem by the 30S head domain. Tandem A-minor interactions form between 16S ribosomal RNA nucleotides A1339 and G1338 and tRNA base pairs G30-C40 and G29-C41, respectively. Swapping the G30-C40 pair of tRNA with C-G reduces discrimination against the noncanonical start codon CUG in vitro, suggesting crosstalk between gripping of the anticodon stem and recognition of the start codon. Here, we solved electron cryomicroscopy structures of E. coli 70S initiation complexes containing an fMet-tRNA G30-C40 variant paired to noncanonical CUG start codon, in the presence or absence of IF2 and the non-hydrolyzable GTP analog GDPCP, alongside structures of 70S initiation complexes containing this tRNA variant paired to the canonical bacterial start codons AUG, GUG, and UUG. We find that the M1 mutation weakens A-minor interactions between tRNA and 16S nucleotides A1339 and G1338, with IF2 strengthening the interaction of G1338 with the tRNA minor groove. These structures suggest how even slight changes to the recognition of the fMet-tRNA anticodon stem by the ribosome can impact start codon selection. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ax8.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9ax8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9ax8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ax8_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 9ax8_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 9ax8_validation.xml.gz | 210.2 KB | Display | |
Data in CIF | 9ax8_validation.cif.gz | 370.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/9ax8 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9ax8 | HTTPS FTP |
-Related structure data
Related structure data | 43930MC 9ax7C 9cg5C 9cg6C 9cg7C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 27 types, 27 molecules 0123456789EFHJKLMNOPQRSTUVY
-RNA chain , 5 types, 5 molecules XaxyA
#27: RNA chain | Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1266940032 |
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#29: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1338015391 |
#50: RNA chain | Mass: 8706.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#51: RNA chain | Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 2260466602 |
#53: RNA chain | Mass: 935101.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#30: Protein | Mass: 24253.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9ZNW8 |
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#31: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V5 |
#32: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR62 |
#33: Protein | Mass: 15804.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: F4TL26 |
#34: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358 |
#35: Protein | Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359 |
#36: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A828U358 |
#37: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3KYI7 |
#38: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0H3EQD3 |
#39: Protein | Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#40: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQR7 |
#41: Protein | Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1P5F8 |
#42: Protein | Mass: 7117.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A090BZT4 |
#43: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XN21 |
#44: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SYP2 |
#45: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080IK26 |
#46: Protein | Mass: 6328.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T9 |
#47: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A7U9LGZ0 |
#48: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TRH7 |
#49: Protein | Mass: 6067.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A5C9AJ78 |
-Protein , 1 types, 1 molecules z
#52: Protein | Mass: 54866.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376TVY0 |
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-Non-polymers , 2 types, 288 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | ChemComp-GCP / | |
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-Details
Has ligand of interest | N |
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-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 70S ribosome in complex with fMet-tRNA-fMet M1, initiation factor 2, and mRNA containing P-site CUG start codon and A-site GUA codon Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42825 / Symmetry type: POINT | |||||||||||||||||||||||||
Atomic model building | PDB-ID: 6O9K Accession code: 6O9K / Source name: PDB / Type: experimental model |