J3_4D5Y_006

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

GCAG*CGUAG*UCCGAC

Length

15 nucleotides

Bulged bases

4D5Y|1|2|A|1592

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

J3_4D5Y_006 not in the Motif Atlas

Homologous match to J3_5TBW_005

Geometric discrepancy: 0.1729

The information below is about J3_5TBW_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_33851.1

Basepair signature

cWW-tSH-F-F-tHS-cWW-cWW-F-F

Number of instances in this motif group

1

Unit IDs

4D5Y|1|2|G|1524
4D5Y|1|2|C|1525
4D5Y|1|2|A|1526
4D5Y|1|2|G|1527
*
4D5Y|1|2|C|1559
4D5Y|1|2|G|1560
4D5Y|1|2|U|1561
4D5Y|1|2|A|1562
4D5Y|1|2|G|1563
*
4D5Y|1|2|U|1588
4D5Y|1|2|C|1589
4D5Y|1|2|C|1590
4D5Y|1|2|G|1591
4D5Y|1|2|A|1592
4D5Y|1|2|C|1593

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain R

60S RIBOSOMAL PROTEIN UL19

Chain g

60S RIBOSOMAL PROTEIN EL34