J3_4D5Y_005

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

UGAACUA*UAG*CGAA

Length

14 nucleotides

Bulged bases

4D5Y|1|2|A|1513, 4D5Y|1|2|G|1620

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_005 not in the Motif Atlas

Homologous match to J3_8C3A_003

Geometric discrepancy: 0.1653

The information below is about J3_8C3A_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_39238.5

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

4D5Y|1|2|U|1510
4D5Y|1|2|G|1511
4D5Y|1|2|A|1512
4D5Y|1|2|A|1513
4D5Y|1|2|C|1514
4D5Y|1|2|U|1515
4D5Y|1|2|A|1516
*
4D5Y|1|2|U|1601
4D5Y|1|2|A|1602
4D5Y|1|2|G|1603
*
4D5Y|1|2|C|1619
4D5Y|1|2|G|1620
4D5Y|1|2|A|1621
4D5Y|1|2|A|1622

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain N

60S RIBOSOMAL PROTEIN EL15

Chain j

60S RIBOSOMAL PROTEIN EL37