2XFZ: Structure of Cytotoxic Domain of Colicin E3 Bound to the 70s Ribosome

Citation:
Abstract
The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.
MMDB ID: 99580
PDB Deposition Date: 2010/5/29
Updated in MMDB: 2013/11 
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Merged PDB IDs:2XFZ 2XG0 2XG1 2XG2
Asymmetric Unit for 2XFZ: 116-meric
Molecular Components in 2XFZ
Label Count Molecule
Proteins (104 molecules)
2
30S Ribosomal Protein S2
Molecule annotation
2
30S Ribosomal Protein S3
Molecule annotation
2
30S Ribosomal Protein S4
Molecule annotation
2
30S Ribosomal Protein S5
Molecule annotation
2
30S Ribosomal Protein S6
Molecule annotation
2
30S Ribosomal Protein S7
Molecule annotation
2
30S Ribosomal Protein S8
Molecule annotation
2
30S Ribosomal Protein S9
Molecule annotation
2
30S Ribosomal Protein S10
Molecule annotation
2
30S Ribosomal Protein S11
Molecule annotation
2
30S Ribosomal Protein S12
Molecule annotation
2
30S Ribosomal Protein S13
Molecule annotation
2
30S Ribosomal Protein S14 Type Z
Molecule annotation
2
30S Ribosomal Protein S15
Molecule annotation
2
30S Ribosomal Protein S16
Molecule annotation
2
30S Ribosomal Protein S17
Molecule annotation
2
30S Ribosomal Protein S18
Molecule annotation
2
30S Ribosomal Protein S19
Molecule annotation
2
30S Ribosomal Protein S20
Molecule annotation
2
30S Ribosomal Protein THX
Molecule annotation
2
Colicin-e3
Molecule annotation
2
50S Ribosomal Protein L27
Molecule annotation
2
50S Ribosomal Protein L28
Molecule annotation
2
50S Ribosomal Protein L29
Molecule annotation
2
50S Ribosomal Protein L30
Molecule annotation
2
50S Ribosomal Protein L31
Molecule annotation
2
50S Ribosomal Protein L32
Molecule annotation
2
50S Ribosomal Protein L33
Molecule annotation
2
50S Ribosomal Protein L34
Molecule annotation
2
50S Ribosomal Protein L35
Molecule annotation
2
50S Ribosomal Protein L36
Molecule annotation
2
50S Ribosomal Protein L1
Molecule annotation
2
50S Ribosomal Protein L2
Molecule annotation
2
50S Ribosomal Protein L3
Molecule annotation
2
50S Ribosomal Protein L4
Molecule annotation
2
50S Ribosomal Protein L5
Molecule annotation
2
50S Ribosomal Protein L6
Molecule annotation
2
50S Ribosomal Protein L9
Molecule annotation
1
50S Ribosomal Protein L10
Molecule annotation
2
50S Ribosomal Protein L13
Molecule annotation
2
50S Ribosomal Protein L14
Molecule annotation
2
50S Ribosomal Protein L15
Molecule annotation
2
50S Ribosomal Protein L16
Molecule annotation
2
50S Ribosomal Protein L17
Molecule annotation
2
50S Ribosomal Protein L18
Molecule annotation
2
50S Ribosomal Protein L19
Molecule annotation
2
50S Ribosomal Protein L20
Molecule annotation
2
50S Ribosomal Protein L21
Molecule annotation
2
50S Ribosomal Protein L22
Molecule annotation
2
50S Ribosomal Protein L23
Molecule annotation
2
50S Ribosomal Protein L24
Molecule annotation
2
50S Ribosomal Protein L25
Molecule annotation
1
50S Ribosomal Protein L10
Molecule annotation
Nucleotides(6 molecules)
2
16S rRNA
Molecule annotation
4
E-site tRNA PHE or P-site tRNA PHE
Molecule annotation
1
mRNA
Molecule annotation
2
RNA (2848-mer)
Molecule annotation
2
RNA (119-mer)
Molecule annotation
1
mRNA
Molecule annotation
Chemicals (2338 molecules)
1
4
2
2334
* Click molecule labels to explore molecular sequence information.

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