IL_4D5Y_064

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

GACCCCAGAAAA*UGAAAAUGGAUGGCGC

Length

28 nucleotides

Bulged bases

4D5Y|1|2|C|1913, 4D5Y|1|2|A|2019

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_064 not in the Motif Atlas

Geometric match to IL_5TBW_052

Geometric discrepancy: 0.2327

The information below is about IL_5TBW_052

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_53762.1

Basepair signature

cWW-tSH-tHH-L-R-L-R-L-R-L-R-L-R-L-R-L-cWW-L-cWW-L

Number of instances in this motif group

2

Unit IDs

4D5Y|1|2|G|1911
4D5Y|1|2|A|1912
4D5Y|1|2|C|1913
4D5Y|1|2|C|1914
4D5Y|1|2|C|1915
4D5Y|1|2|C|1916
4D5Y|1|2|A|1917
4D5Y|1|2|G|1918
4D5Y|1|2|A|1919
4D5Y|1|2|A|1920
4D5Y|1|2|A|1921
4D5Y|1|2|A|1922
*
4D5Y|1|2|U|2016
4D5Y|1|2|G|2017
4D5Y|1|2|A|2018
4D5Y|1|2|A|2019
4D5Y|1|2|A|2020
4D5Y|1|2|A|2021
4D5Y|1|2|U|2022
4D5Y|1|2|G|2023
4D5Y|1|2|G|2024
4D5Y|1|2|A|2025
4D5Y|1|2|U|2026
4D5Y|1|2|G|2027
4D5Y|1|2|G|2028
4D5Y|1|2|C|2029
4D5Y|1|2|G|2030
4D5Y|1|2|C|2031

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 4

5S ribosomal RNA; 5S rRNA

Chain B

60S RIBOSOMAL PROTEIN UL3

Chain I

60S RIBOSOMAL PROTEIN UL16

Chain O

60S RIBOSOMAL PROTEIN UL13

Chain f

60S RIBOSOMAL PROTEIN EL33

Chain m

60S RIBOSOMAL PROTEIN EL40