J3_8VTX_056

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

8VTX|1|2A|U|504, 8VTX|1|2A|G|508

QA status

Valid loop

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

J3_8VTX_056 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.052

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

8VTX|1|2A|G|30
8VTX|1|2A|C|31
*
8VTX|1|2A|G|474
8VTX|1|2A|U|475
8VTX|1|2A|G|476
8VTX|1|2A|A|477
8VTX|1|2A|A|478
8VTX|1|2A|A|479
8VTX|1|2A|A|480
8VTX|1|2A|G|481
8VTX|1|2A|A|482
8VTX|1|2A|A|483
8VTX|1|2A|C|484
*
8VTX|1|2A|G|496
8VTX|1|2A|A|497
8VTX|1|2A|G|498
8VTX|1|2A|U|499
8VTX|1|2A|G|500
8VTX|1|2A|A|501
8VTX|1|2A|A|502
8VTX|1|2A|A|503
8VTX|1|2A|U|504
8VTX|1|2A|A|505
8VTX|1|2A|G|506
8VTX|1|2A|A|507
8VTX|1|2A|G|508
8VTX|1|2A|C|509
8VTX|1|2A|C|510

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24