J3_4D5Y_002

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

CUCUCCC*GCCACGCGC*GCGGAG

Length

22 nucleotides

Bulged bases

4D5Y|1|2|U|966, 4D5Y|1|2|C|967, 4D5Y|1|2|C|968, 4D5Y|1|2|C|1216, 4D5Y|1|2|C|1217, 4D5Y|1|2|A|1218

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|963
4D5Y|1|2|U|964
4D5Y|1|2|C|965
4D5Y|1|2|U|966
4D5Y|1|2|C|967
4D5Y|1|2|C|968
4D5Y|1|2|C|969
*
4D5Y|1|2|G|1215
4D5Y|1|2|C|1216
4D5Y|1|2|C|1217
4D5Y|1|2|A|1218
4D5Y|1|2|C|1219
4D5Y|1|2|G|1220
4D5Y|1|2|C|1221
4D5Y|1|2|G|1222
4D5Y|1|2|C|1223
*
4D5Y|1|2|G|1246
4D5Y|1|2|C|1247
4D5Y|1|2|G|1248
4D5Y|1|2|G|1249
4D5Y|1|2|A|1250
4D5Y|1|2|G|1251

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain F

60S RIBOSOMAL PROTEIN UL30