J4_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

CAAAUAU*AGG*CAUGUU*AG

Length

18 nucleotides

Bulged bases

4D5Y|1|2|A|2343, 4D5Y|1|2|U|2346, 4D5Y|1|2|A|2347, 4D5Y|1|2|U|2803, 4D5Y|1|2|U|2805

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|2342
4D5Y|1|2|A|2343
4D5Y|1|2|A|2344
4D5Y|1|2|A|2345
4D5Y|1|2|U|2346
4D5Y|1|2|A|2347
4D5Y|1|2|U|2348
*
4D5Y|1|2|A|2366
4D5Y|1|2|G|2367
4D5Y|1|2|G|2368
*
4D5Y|1|2|C|2801
4D5Y|1|2|A|2802
4D5Y|1|2|U|2803
4D5Y|1|2|G|2804
4D5Y|1|2|U|2805
4D5Y|1|2|U|2806
*
4D5Y|1|2|A|3825
4D5Y|1|2|G|3826

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain P

60S RIBOSOMAL PROTEIN UL22

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain d

60S RIBOSOMAL PROTEIN EL31