J3_4D5Y_043

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

GGCGGAGAU*AGU*AGGGUGUAAAUCUC

Length

26 nucleotides

Bulged bases

4D5Y|1|2|A|2528, 4D5Y|1|2|G|2551, 4D5Y|1|2|G|2736, 4D5Y|1|2|G|2739

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|2523
4D5Y|1|2|G|2524
4D5Y|1|2|C|2525
4D5Y|1|2|G|2526
4D5Y|1|2|G|2527
4D5Y|1|2|A|2528
4D5Y|1|2|G|2529
4D5Y|1|2|A|2530
4D5Y|1|2|U|2531
*
4D5Y|1|2|A|2550
4D5Y|1|2|G|2551
4D5Y|1|2|U|2552
*
4D5Y|1|2|A|2734
4D5Y|1|2|G|2735
4D5Y|1|2|G|2736
4D5Y|1|2|G|2737
4D5Y|1|2|U|2738
4D5Y|1|2|G|2739
4D5Y|1|2|U|2740
4D5Y|1|2|A|2741
4D5Y|1|2|A|2742
4D5Y|1|2|A|2743
4D5Y|1|2|U|2744
4D5Y|1|2|C|2745
4D5Y|1|2|U|2746
4D5Y|1|2|C|2747

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain Z

60S RIBOSOMAL PROTEIN EL27

Chain g

60S RIBOSOMAL PROTEIN EL34

Chain k

60S RIBOSOMAL PROTEIN EL38