HL_4D5Y_089

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

AGCAGAAU

Length

8 nucleotides

Bulged bases

4D5Y|1|2|G|4435

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

HL_4D5Y_089 not in the Motif Atlas

Homologous match to HL_8P9A_173

Geometric discrepancy: 0.3238

The information below is about HL_8P9A_173

Detailed Annotation

GNRA variation

Broad Annotation

GNRA variation

Motif group

HL_31585.4

Basepair signature

cWW-F-F-F-F-F

Number of instances in this motif group

20

Unit IDs

4D5Y|1|2|A|4434
4D5Y|1|2|G|4435
4D5Y|1|2|C|4436
4D5Y|1|2|A|4437
4D5Y|1|2|G|4438
4D5Y|1|2|A|4439
4D5Y|1|2|A|4440
4D5Y|1|2|U|4441

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain H

60S RIBOSOMAL PROTEIN UL6

Chain m

60S RIBOSOMAL PROTEIN EL40