4DR6: Crystal Structure Of The Thermus Thermophilus (hb8) 30s Ribosomal Subunit With Codon, Near-cognate Transfer Rna Anticodon Stem-loop Mismatched At The First Codon Position And Streptomycin Bound

Citation:
Abstract
During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.
PDB ID: 4DR6Download
MMDB ID: 105029
PDB Deposition Date: 2012/2/16
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 3.3  Å
Source Organism:
Similar Structures:
Biological Unit for 4DR6: 25-meric; determined by author
Molecular Components in 4DR6
Label Count Molecule
Proteins (20 molecules)
1
30S Ribosomal Protein S2(Gene symbol: rpsB)
Molecule annotation
1
30S Ribosomal Protein S3(Gene symbol: rpsC)
Molecule annotation
1
30S Ribosomal Protein S4(Gene symbol: rpsD)
Molecule annotation
1
30S Ribosomal Protein S5(Gene symbol: rpsE)
Molecule annotation
1
30S Ribosomal Protein S6(Gene symbol: rpsF)
Molecule annotation
1
30S Ribosomal Protein S7(Gene symbol: TTHA1696)
Molecule annotation
1
30S Ribosomal Protein S8
Molecule annotation
1
30S Ribosomal Protein S9(Gene symbol: rpsI)
Molecule annotation
1
30S Ribosomal Protein S10(Gene symbol: rpsJ)
Molecule annotation
1
30S Ribosomal Protein S11(Gene symbol: TTHA1666)
Molecule annotation
1
30S Ribosomal Protein S12
Molecule annotation
1
30S Ribosomal Protein S13(Gene symbol: rpsM)
Molecule annotation
1
30S Ribosomal Protein S14
Molecule annotation
1
30S Ribosomal Protein S15(Gene symbol: rpsO)
Molecule annotation
1
30S Ribosomal Protein S16(Gene symbol: rpsP)
Molecule annotation
1
30S Ribosomal Protein S17
Molecule annotation
1
30S Ribosomal Protein S18(Gene symbol: rpsR)
Molecule annotation
1
30S Ribosomal Protein S19(Gene symbol: rpsS)
Molecule annotation
1
30S Ribosomal Protein S20(Gene symbol: rpsT)
Molecule annotation
1
30S Ribosomal Protein THX(Gene symbol: TTHA1396)
Molecule annotation
Nucleotides(5 molecules)
1
16S rRNA
Molecule annotation
1
5'-r(*up*up*up*u)-3'
Molecule annotation
1
5'-r(p*up*up*gp*ap*gp*gp*(psu)p*gp*g)-3'
Molecule annotation
1
5'-r(p*cp*up*up*gp*ap*gp*gp*(psu)p*gp*gp*u)-3'
Molecule annotation
1
5'-r(*up*up*u)-3'
Molecule annotation
Chemicals (379 molecules)
1
376
2
1
3
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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