J3_4D5Y_039

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

CCUCC*GGCCAC*GAGGUUCUCUCGG

Length

24 nucleotides

Bulged bases

4D5Y|1|2|U|973, 4D5Y|1|2|A|1202, 4D5Y|1|2|U|1205, 4D5Y|1|2|U|1208, 4D5Y|1|2|C|1209, 4D5Y|1|2|U|1210, 4D5Y|1|2|C|1211

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

4D5Y|1|2|C|971
4D5Y|1|2|C|972
4D5Y|1|2|U|973
4D5Y|1|2|C|974
4D5Y|1|2|C|975
*
4D5Y|1|2|G|1054
4D5Y|1|2|G|1055
4D5Y|1|2|C|1056
4D5Y|1|2|C|1057
4D5Y|1|2|A|1058
4D5Y|1|2|C|1059
*
4D5Y|1|2|G|1201
4D5Y|1|2|A|1202
4D5Y|1|2|G|1203
4D5Y|1|2|G|1204
4D5Y|1|2|U|1205
4D5Y|1|2|U|1206
4D5Y|1|2|C|1207
4D5Y|1|2|U|1208
4D5Y|1|2|C|1209
4D5Y|1|2|U|1210
4D5Y|1|2|C|1211
4D5Y|1|2|G|1212
4D5Y|1|2|G|1213

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain F

60S RIBOSOMAL PROTEIN UL30