J4_8VTX_031

3D structure

PDB id

8VTX (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with macrolone MCX-128, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.4 Å

Loop

Sequence

G(4SU)GG*CGU*AAGGUCG*CC

Length

16 nucleotides

Bulged bases

8VTX|1|2x|4SU|8, 8VTX|1|2x|U|47, 8VTX|1|2x|C|48

QA status

Modified nucleotides: 4SU

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

J4_8VTX_031 not in the Motif Atlas

Homologous match to J4_9DFC_015

Geometric discrepancy: 0.0961

The information below is about J4_9DFC_015

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_70449.29

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

54

Unit IDs

8VTX|1|2x|G|7
8VTX|1|2x|4SU|8
8VTX|1|2x|G|9
8VTX|1|2x|G|10
*
8VTX|1|2x|C|25
8VTX|1|2x|G|26
8VTX|1|2x|U|27
*
8VTX|1|2x|A|43
8VTX|1|2x|A|44
8VTX|1|2x|G|45
8VTX|1|2x|G|46
8VTX|1|2x|U|47
8VTX|1|2x|C|48
8VTX|1|2x|G|49
*
8VTX|1|2x|C|65
8VTX|1|2x|C|66

Current chains

Chain 2x

Aminoacylated fMet-tRNAmet

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA

Chain 2Q

50S ribosomal protein L16

Chain 2a

Small subunit ribosomal RNA; SSU rRNA

Chain 2m

30S ribosomal protein S13