J4_4D5Y_005

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

GGGA*UUUGUGAAGGGCAGGG*CCCGUGCCUUGGAAAG*UC

Length

38 nucleotides

Bulged bases

4D5Y|1|2|A|2673

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|2595
4D5Y|1|2|G|2596
4D5Y|1|2|G|2597
4D5Y|1|2|A|2598
*
4D5Y|1|2|U|2612
4D5Y|1|2|U|2613
4D5Y|1|2|U|2614
4D5Y|1|2|G|2615
4D5Y|1|2|U|2616
4D5Y|1|2|G|2617
4D5Y|1|2|A|2618
4D5Y|1|2|A|2619
4D5Y|1|2|G|2620
4D5Y|1|2|G|2621
4D5Y|1|2|G|2622
4D5Y|1|2|C|2623
4D5Y|1|2|A|2624
4D5Y|1|2|G|2625
4D5Y|1|2|G|2626
4D5Y|1|2|G|2627
*
4D5Y|1|2|C|2660
4D5Y|1|2|C|2661
4D5Y|1|2|C|2662
4D5Y|1|2|G|2663
4D5Y|1|2|U|2664
4D5Y|1|2|G|2665
4D5Y|1|2|C|2666
4D5Y|1|2|C|2667
4D5Y|1|2|U|2668
4D5Y|1|2|U|2669
4D5Y|1|2|G|2670
4D5Y|1|2|G|2671
4D5Y|1|2|A|2672
4D5Y|1|2|A|2673
4D5Y|1|2|A|2674
4D5Y|1|2|G|2675
*
4D5Y|1|2|U|2695
4D5Y|1|2|C|2696

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain U

60S RIBOSOMAL PROTEIN EL22

Chain g

60S RIBOSOMAL PROTEIN EL34

Chain k

60S RIBOSOMAL PROTEIN EL38