J3_4D5Y_036

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

UUGAAAAGAACUUU*AGAGAGUUCAAGAGGGCGUGAAAC*GUGGAUCA

Length

46 nucleotides

Bulged bases

4D5Y|1|2|A|380, 4D5Y|1|2|G|400, 4D5Y|1|2|G|404

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|U|371
4D5Y|1|2|U|372
4D5Y|1|2|G|373
4D5Y|1|2|A|374
4D5Y|1|2|A|375
4D5Y|1|2|A|376
4D5Y|1|2|A|377
4D5Y|1|2|G|378
4D5Y|1|2|A|379
4D5Y|1|2|A|380
4D5Y|1|2|C|381
4D5Y|1|2|U|382
4D5Y|1|2|U|383
4D5Y|1|2|U|384
*
4D5Y|1|2|A|389
4D5Y|1|2|G|390
4D5Y|1|2|A|391
4D5Y|1|2|G|392
4D5Y|1|2|A|393
4D5Y|1|2|G|394
4D5Y|1|2|U|395
4D5Y|1|2|U|396
4D5Y|1|2|C|397
4D5Y|1|2|A|398
4D5Y|1|2|A|399
4D5Y|1|2|G|400
4D5Y|1|2|A|401
4D5Y|1|2|G|402
4D5Y|1|2|G|403
4D5Y|1|2|G|404
4D5Y|1|2|C|405
4D5Y|1|2|G|406
4D5Y|1|2|U|407
4D5Y|1|2|G|408
4D5Y|1|2|A|409
4D5Y|1|2|A|410
4D5Y|1|2|A|411
4D5Y|1|2|C|412
*
4D5Y|1|3|G|13
4D5Y|1|3|U|14
4D5Y|1|3|G|15
4D5Y|1|3|G|16
4D5Y|1|3|A|17
4D5Y|1|3|U|18
4D5Y|1|3|C|19
4D5Y|1|3|A|20

Current chains

Chain 2

28S Ribosomal RNA

Chain 3

5.8S Ribosomal RNA

Nearby chains

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain P

60S RIBOSOMAL PROTEIN UL22

Chain Y

60S RIBOSOMAL PROTEIN UL24

Chain e

60S RIBOSOMAL PROTEIN EL32

Chain l

60S RIBOSOMAL PROTEIN EL39