J5_4D5Y_004

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

AGAAGACC*GGAUAACUGGCU*GAUCCUUCGAUGU*GUUUAGA*UUAGUUU

Length

47 nucleotides

Bulged bases

4D5Y|1|2|A|3875, 4D5Y|1|2|A|4354, 4D5Y|1|2|U|4355, 4D5Y|1|2|G|4408, 4D5Y|1|2|U|4410, 4D5Y|1|2|U|4515

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|A|3872
4D5Y|1|2|G|3873
4D5Y|1|2|A|3874
4D5Y|1|2|A|3875
4D5Y|1|2|G|3876
4D5Y|1|2|A|3877
4D5Y|1|2|C|3878
4D5Y|1|2|C|3879
*
4D5Y|1|2|G|4352
4D5Y|1|2|G|4353
4D5Y|1|2|A|4354
4D5Y|1|2|U|4355
4D5Y|1|2|A|4356
4D5Y|1|2|A|4357
4D5Y|1|2|C|4358
4D5Y|1|2|U|4359
4D5Y|1|2|G|4360
4D5Y|1|2|G|4361
4D5Y|1|2|C|4362
4D5Y|1|2|U|4363
*
4D5Y|1|2|G|4400
4D5Y|1|2|A|4401
4D5Y|1|2|U|4402
4D5Y|1|2|C|4403
4D5Y|1|2|C|4404
4D5Y|1|2|U|4405
4D5Y|1|2|U|4406
4D5Y|1|2|C|4407
4D5Y|1|2|G|4408
4D5Y|1|2|A|4409
4D5Y|1|2|U|4410
4D5Y|1|2|G|4411
4D5Y|1|2|U|4412
*
4D5Y|1|2|G|4489
4D5Y|1|2|U|4490
4D5Y|1|2|U|4491
4D5Y|1|2|U|4492
4D5Y|1|2|A|4493
4D5Y|1|2|G|4494
4D5Y|1|2|A|4495
*
4D5Y|1|2|U|4511
4D5Y|1|2|U|4512
4D5Y|1|2|A|4513
4D5Y|1|2|G|4514
4D5Y|1|2|U|4515
4D5Y|1|2|U|4516
4D5Y|1|2|U|4517

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain B

60S RIBOSOMAL PROTEIN UL3

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain I

60S RIBOSOMAL PROTEIN UL16

Chain P

60S RIBOSOMAL PROTEIN UL22

Chain b

60S RIBOSOMAL PROTEIN EL29