J3_4D5Y_020

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

GGGUCCGCGCAGUCC*GGUGCG*CGACGUCGGCUACC

Length

35 nucleotides

Bulged bases

4D5Y|1|2|U|436, 4D5Y|1|2|G|441, 4D5Y|1|2|C|1281, 4D5Y|1|2|U|1282, 4D5Y|1|2|A|1283

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|G|433
4D5Y|1|2|G|434
4D5Y|1|2|G|435
4D5Y|1|2|U|436
4D5Y|1|2|C|437
4D5Y|1|2|C|438
4D5Y|1|2|G|439
4D5Y|1|2|C|440
4D5Y|1|2|G|441
4D5Y|1|2|C|442
4D5Y|1|2|A|443
4D5Y|1|2|G|444
4D5Y|1|2|U|445
4D5Y|1|2|C|446
4D5Y|1|2|C|447
*
4D5Y|1|2|G|688
4D5Y|1|2|G|689
4D5Y|1|2|U|690
4D5Y|1|2|G|691
4D5Y|1|2|C|692
4D5Y|1|2|G|693
*
4D5Y|1|2|C|1272
4D5Y|1|2|G|1273
4D5Y|1|2|A|1274
4D5Y|1|2|C|1275
4D5Y|1|2|G|1276
4D5Y|1|2|U|1277
4D5Y|1|2|C|1278
4D5Y|1|2|G|1279
4D5Y|1|2|G|1280
4D5Y|1|2|C|1281
4D5Y|1|2|U|1282
4D5Y|1|2|A|1283
4D5Y|1|2|C|1284
4D5Y|1|2|C|1285

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 3

5.8S ribosomal RNA; 5.8S rRNA

Chain E

60S RIBOSOMAL PROTEIN EL6

Chain e

60S RIBOSOMAL PROTEIN EL32

Chain f

60S RIBOSOMAL PROTEIN EL33

Chain t

60S RIBOSOMAL PROTEIN EL28