HL_4D5Y_031

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

ACGAGAACU

Length

9 nucleotides

Bulged bases

4D5Y|1|2|A|2359, 4D5Y|1|2|C|2360

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_031 not in the Motif Atlas

Homologous match to HL_5TBW_031

Geometric discrepancy: 0.2075

The information below is about HL_5TBW_031

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_43993.1

Basepair signature

cWW-tWH-F-F-F-F-F

Number of instances in this motif group

141

Unit IDs

4D5Y|1|2|A|2353
4D5Y|1|2|C|2354
4D5Y|1|2|G|2355
4D5Y|1|2|A|2356
4D5Y|1|2|G|2357
4D5Y|1|2|A|2358
4D5Y|1|2|A|2359
4D5Y|1|2|C|2360
4D5Y|1|2|U|2361

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain d

60S RIBOSOMAL PROTEIN EL31