HL_4D5Y_086

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

AGCAGUU

Length

7 nucleotides

Bulged bases

4D5Y|1|2|G|2398, 4D5Y|1|2|U|2402

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_086 not in the Motif Atlas

Homologous match to HL_8P9A_144

Geometric discrepancy: 0.3297

The information below is about HL_8P9A_144

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_57176.2

Basepair signature

cWW-F-F-F

Number of instances in this motif group

14

Unit IDs

4D5Y|1|2|A|2397
4D5Y|1|2|G|2398
4D5Y|1|2|C|2399
4D5Y|1|2|A|2400
4D5Y|1|2|G|2401
4D5Y|1|2|U|2402
4D5Y|1|2|U|2403

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain P

60S RIBOSOMAL PROTEIN UL22

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain l

60S RIBOSOMAL PROTEIN EL39