IL_4D5Y_092

3D structure

PDB id

4D5Y (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

Experimental method

ELECTRON MICROSCOPY

Resolution

9 Å

Loop

Sequence

CGAAGG*UGUUGACG

Length

14 nucleotides

Bulged bases

4D5Y|1|2|A|3632, 4D5Y|1|2|U|3648, 4D5Y|1|2|C|3652

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

IL_4D5Y_092 not in the Motif Atlas

Homologous match to IL_5TBW_083

Geometric discrepancy: 0.1755

The information below is about IL_5TBW_083

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_64509.1

Basepair signature

cWW-tWW-tWW-tSS-L-cWW

Number of instances in this motif group

2

Unit IDs

4D5Y|1|2|C|3629
4D5Y|1|2|G|3630
4D5Y|1|2|A|3631
4D5Y|1|2|A|3632
4D5Y|1|2|G|3633
4D5Y|1|2|G|3634
*
4D5Y|1|2|U|3646
4D5Y|1|2|G|3647
4D5Y|1|2|U|3648
4D5Y|1|2|U|3649
4D5Y|1|2|G|3650
4D5Y|1|2|A|3651
4D5Y|1|2|C|3652
4D5Y|1|2|G|3653

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain p

60S RIBOSOMAL PROTEIN EL43