IL_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

GGAA*UC

Length

6 nucleotides

Bulged bases

None detected

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

IL_4D5Y_086 not in the Motif Atlas

Geometric match to IL_5TBW_076

Geometric discrepancy: 0.1873

The information below is about IL_5TBW_076

Detailed Annotation

Major groove platform; stack outside cWW

Broad Annotation

Major groove platform

Motif group

IL_50694.4

Basepair signature

cWW-cWW-tSH-cWW-R

Number of instances in this motif group

28

Unit IDs

4D5Y|1|2|G|2824
4D5Y|1|2|G|2825
4D5Y|1|2|A|2826
4D5Y|1|2|A|2827
*
4D5Y|1|2|U|3809
4D5Y|1|2|C|3810

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain B

60S RIBOSOMAL PROTEIN UL3

Chain V

60S RIBOSOMAL PROTEIN UL14