IL_4D5Y_176

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

GGCGAAG*UGGAGGUC

Length

15 nucleotides

Bulged bases

4D5Y|1|2|G|1556

QA status

Unknown status

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_176 not in the Motif Atlas

Geometric match to IL_8VTW_001

Geometric discrepancy: 0.3942

The information below is about IL_8VTW_001

Detailed Annotation

Triple sheared with non-canonical cWW

Broad Annotation

Triple sheared

Motif group

IL_66414.7

Basepair signature

cWW-L-R-tSH-tSH-tHS-cWW-cWW

Number of instances in this motif group

7

Unit IDs

4D5Y|1|2|G|1528
4D5Y|1|2|G|1529
4D5Y|1|2|C|1530
4D5Y|1|2|G|1531
4D5Y|1|2|A|1532
4D5Y|1|2|A|1533
4D5Y|1|2|G|1534
*
4D5Y|1|2|U|1551
4D5Y|1|2|G|1552
4D5Y|1|2|G|1553
4D5Y|1|2|A|1554
4D5Y|1|2|G|1555
4D5Y|1|2|G|1556
4D5Y|1|2|U|1557
4D5Y|1|2|C|1558

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain p

60S RIBOSOMAL PROTEIN EL43