J4_9DFD_013

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

GGG*CGAAAG*CCCUAAACGAUG*CC

Length

23 nucleotides

Bulged bases

9DFD|1|1a|A|815

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

J4_9DFD_013 not in the Motif Atlas

Homologous match to J4_4LFB_003

Geometric discrepancy: 0.0505

The information below is about J4_4LFB_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_14595.1

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F

Number of instances in this motif group

5

Unit IDs

9DFD|1|1a|G|575
9DFD|1|1a|G|576
9DFD|1|1a|G|577
*
9DFD|1|1a|C|764
9DFD|1|1a|G|765
9DFD|1|1a|A|766
9DFD|1|1a|A|767
9DFD|1|1a|A|768
9DFD|1|1a|G|769
*
9DFD|1|1a|C|810
9DFD|1|1a|C|811
9DFD|1|1a|C|812
9DFD|1|1a|U|813
9DFD|1|1a|A|814
9DFD|1|1a|A|815
9DFD|1|1a|A|816
9DFD|1|1a|C|817
9DFD|1|1a|G|818
9DFD|1|1a|A|819
9DFD|1|1a|U|820
9DFD|1|1a|G|821
*
9DFD|1|1a|C|879
9DFD|1|1a|C|880

Current chains

Chain 1a

16S Ribosomal RNA

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA

Chain 1h

30S ribosomal protein S8

Chain 1l

30S ribosomal protein S12

Chain 1o

30S ribosomal protein S15

Chain 1q

30S ribosomal protein S17