J3_9DFC_039

3D structure

PDB id

9DFC (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.5 Å

Loop

Sequence

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

9DFC|1|2A|U|504, 9DFC|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_9DFC_039 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0596

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_92134.2

Basepair signature

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

Number of instances in this motif group

6

Unit IDs

9DFC|1|2A|G|30
9DFC|1|2A|C|31
*
9DFC|1|2A|G|474
9DFC|1|2A|U|475
9DFC|1|2A|G|476
9DFC|1|2A|A|477
9DFC|1|2A|A|478
9DFC|1|2A|A|479
9DFC|1|2A|A|480
9DFC|1|2A|G|481
9DFC|1|2A|A|482
9DFC|1|2A|A|483
9DFC|1|2A|C|484
*
9DFC|1|2A|G|496
9DFC|1|2A|A|497
9DFC|1|2A|G|498
9DFC|1|2A|U|499
9DFC|1|2A|G|500
9DFC|1|2A|A|501
9DFC|1|2A|A|502
9DFC|1|2A|A|503
9DFC|1|2A|U|504
9DFC|1|2A|A|505
9DFC|1|2A|G|506
9DFC|1|2A|A|507
9DFC|1|2A|G|508
9DFC|1|2A|C|509
9DFC|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