J4_9DFD_007

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

GACUG*CACAG*CGAC*GUAAC

Length

19 nucleotides

Bulged bases

None detected

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_007 not in the Motif Atlas

Homologous match to J4_5J7L_025

Geometric discrepancy: 0.0457

The information below is about J4_5J7L_025

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.5

Basepair signature

cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

Number of instances in this motif group

4

Unit IDs

9DFD|1|1A|G|1772
9DFD|1|1A|A|1773
9DFD|1|1A|C|1774
9DFD|1|1A|U|1775
9DFD|1|1A|G|1776
*
9DFD|1|1A|C|1788
9DFD|1|1A|A|1789
9DFD|1|1A|C|1790
9DFD|1|1A|A|1791
9DFD|1|1A|G|1792
*
9DFD|1|1A|C|1827
9DFD|1|1A|G|1828
9DFD|1|1A|A|1829
9DFD|1|1A|C|1830
*
9DFD|1|1A|G|1975
9DFD|1|1A|U|1976
9DFD|1|1A|A|1977
9DFD|1|1A|A|1978
9DFD|1|1A|C|1979

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1D

50S ribosomal protein L2

Chain 1a

Small subunit ribosomal RNA; SSU rRNA