J3_9DFD_072

3D structure

PDB id

9DFD (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 B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

9DFD|1|2a|U|1240, 9DFD|1|2a|U|1302

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_9DFD_072 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.087

The information below is about J3_4LFB_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_03192.1

Basepair signature

cWW-cSS-tHW-F-F-F-cWW-cWW-cSH-cSH-F

Number of instances in this motif group

5

Unit IDs

9DFD|1|2a|C|1237
9DFD|1|2a|A|1238
9DFD|1|2a|A|1239
9DFD|1|2a|U|1240
9DFD|1|2a|G|1241
*
9DFD|1|2a|C|1296
9DFD|1|2a|C|1297
9DFD|1|2a|C|1298
9DFD|1|2a|A|1299
9DFD|1|2a|G|1300
9DFD|1|2a|U|1301
9DFD|1|2a|U|1302
9DFD|1|2a|C|1303
*
9DFD|1|2a|G|1334
9DFD|1|2a|C|1335
9DFD|1|2a|C|1336
9DFD|1|2a|G|1337

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2g

30S ribosomal protein S7

Chain 2m

30S ribosomal protein S13

Chain 2u

30S ribosomal protein Thx