ISDA

Deposition Date 2005-04-11

Release Date 2005-04-19

Last Version Date 2024-02-14

Entry Detail

PDB ID:

1ZC8

Keywords:

RNA binding protein/RNA

Title:

Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 274)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

13.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:TLD 16S ribosomal RNA
Chain IDs:A
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:H2 16S rRNA
Chain IDs:B
Chain Length:16
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:H2b d mRNA
Chain IDs:C
Chain Length:31
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:H5 16S ribosomal RNA
Chain IDs:E (auth: F)
Chain Length:29
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:protein kinase 4 mRNA
Chain IDs:D (auth: G)
Chain Length:30
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:protein kinase 2 mRNA
Chain IDs:F (auth: H)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:protein kinase 3
Chain IDs:G (auth: I)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:protein kinase 4 mRNA
Chain IDs:H (auth: J)
Chain Length:52
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:SsrA-binding protein
Chain IDs:J (auth: K)
Chain Length:130
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:O66640 Pfam ID:PF01668

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor Tu
Chain IDs:K (auth: Y)
Chain Length:405
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN6 Pfam ID:PF00009, PF03144, PF03143

Polymer Type:polyribonucleotide
Molecule:H44 16S ribosomal RNA
Chain IDs:I (auth: Z)
Chain Length:91
Number of Molecules:1
Biological Source:Thermus thermophilus

Ligand Molecules

Primary Citation

Visualizing tmRNA Entry into a Stalled Ribosome

Valle, M, Gillet, R, Kaur, S, Henne, A, Ramakrishnan, V, Frank, J, Dong, G, Nowakowski, J, Hoffman, D.W, Knudsen, B, Wower, J, Zwieb, C, Gorodkin, J, Valle, M, Sengupta, J, Swami, N.K, Grassucci, R.A, Burkhardt, N, Nierhaus, K.H, Agrawal, R.K, Frank, J, Nissen, P, Kjeldgaard, M, Thirup, S, Nyborg, J, Ogle, J.M, Murphy Iv, F.V, Tarry, M.J, Ramakrishnan, V.Show

Science 300 127 130 (2003)

PMID: 12677067 DOI: 10.1126/science.1081798

Abstact

Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.

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Primary Citation of related structures