J4_4D5Y_001

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

CCCAAGUCC*GGCCCAGCCC*GAC*GGUAGCGG

Length

30 nucleotides

Bulged bases

4D5Y|1|2|U|197, 4D5Y|1|2|C|213, 4D5Y|1|2|C|214

QA status

Unknown status

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|191
4D5Y|1|2|C|192
4D5Y|1|2|C|193
4D5Y|1|2|A|194
4D5Y|1|2|A|195
4D5Y|1|2|G|196
4D5Y|1|2|U|197
4D5Y|1|2|C|198
4D5Y|1|2|C|199
*
4D5Y|1|2|G|210
4D5Y|1|2|G|211
4D5Y|1|2|C|212
4D5Y|1|2|C|213
4D5Y|1|2|C|214
4D5Y|1|2|A|215
4D5Y|1|2|G|216
4D5Y|1|2|C|217
4D5Y|1|2|C|218
4D5Y|1|2|C|219
*
4D5Y|1|2|G|223
4D5Y|1|2|A|224
4D5Y|1|2|C|225
*
4D5Y|1|2|G|237
4D5Y|1|2|G|238
4D5Y|1|2|U|239
4D5Y|1|2|A|240
4D5Y|1|2|G|241
4D5Y|1|2|C|242
4D5Y|1|2|G|243
4D5Y|1|2|G|244

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 3

5.8S ribosomal RNA; 5.8S rRNA

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain Y

60S RIBOSOMAL PROTEIN UL24

Chain j

60S RIBOSOMAL PROTEIN EL37