J3_4D5Y_038

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

CGACC*GAGGGAGCGAGACCCGUC*GCACGGGGUCGG

Length

35 nucleotides

Bulged bases

4D5Y|1|2|G|941, 4D5Y|1|2|A|944, 4D5Y|1|2|A|950, 4D5Y|1|2|G|1262

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|697
4D5Y|1|2|G|698
4D5Y|1|2|A|699
4D5Y|1|2|C|700
4D5Y|1|2|C|701
*
4D5Y|1|2|G|939
4D5Y|1|2|A|940
4D5Y|1|2|G|941
4D5Y|1|2|G|942
4D5Y|1|2|G|943
4D5Y|1|2|A|944
4D5Y|1|2|G|945
4D5Y|1|2|C|946
4D5Y|1|2|G|947
4D5Y|1|2|A|948
4D5Y|1|2|G|949
4D5Y|1|2|A|950
4D5Y|1|2|C|951
4D5Y|1|2|C|952
4D5Y|1|2|C|953
4D5Y|1|2|G|954
4D5Y|1|2|U|955
4D5Y|1|2|C|956
*
4D5Y|1|2|G|1257
4D5Y|1|2|C|1258
4D5Y|1|2|A|1259
4D5Y|1|2|C|1260
4D5Y|1|2|G|1261
4D5Y|1|2|G|1262
4D5Y|1|2|G|1263
4D5Y|1|2|G|1264
4D5Y|1|2|U|1265
4D5Y|1|2|C|1266
4D5Y|1|2|G|1267
4D5Y|1|2|G|1268

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain E

60S RIBOSOMAL PROTEIN EL6

Chain F

60S RIBOSOMAL PROTEIN UL30

Chain e

60S RIBOSOMAL PROTEIN EL32

Chain f

60S RIBOSOMAL PROTEIN EL33

Chain t

60S RIBOSOMAL PROTEIN EL28