- EMDB-1004: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu ... -
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Basic information
Entry
Database: EMDB / ID: EMD-1004
Title
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Map data
70S ribosome stalled by the antibiotic kirromycin
Sample
Sample: Kirromycin stalled 70S Ribosome from E.coli
Complex: 70S Ribosome
Ligand: EF-Tu, tRNA, GTP
RNA: formyl-methionyl tRNA
Function / homology
Function and homology information
endo-alpha-N-acetylgalactosaminidase activity / misfolded RNA binding / Group I intron splicing / RNA folding / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding ...endo-alpha-N-acetylgalactosaminidase activity / misfolded RNA binding / Group I intron splicing / RNA folding / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Protein of unknown function DUF5696 / Family of unknown function (DUF5696) / Endo-alpha-N-acetylgalactosaminidase / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S12/S23 / Ribosomal protein S13-like, H2TH / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS13 / Elongation factor Tu / Alpha-N-acetylgalactosaminidase Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
single particle reconstruction / cryo EM / Resolution: 13.0 Å
Journal: Nat Struct Biol / Year: 2002 Title: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Authors: Holger Stark / Marina V Rodnina / Hans-Joachim Wieden / Friedrich Zemlin / Wolfgang Wintermeyer / Marin van Heel / Abstract: The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional ...The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.
History
Deposition
Aug 27, 2002
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Header (metadata) release
Aug 29, 2002
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Map release
Aug 29, 2003
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Update
Oct 17, 2012
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Current status
Oct 17, 2012
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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