J3_4D5Y_014

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

CAU*GCUUCUG*CAAG

Length

14 nucleotides

Bulged bases

4D5Y|1|2|U|4946

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_014 not in the Motif Atlas

Geometric match to J3_5TBW_069

Geometric discrepancy: 0.1725

The information below is about J3_5TBW_069

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_42762.1

Basepair signature

cWW-cWW-F-cWW-F-F-F-cWW-F

Number of instances in this motif group

1

Unit IDs

4D5Y|1|2|C|4925
4D5Y|1|2|A|4926
4D5Y|1|2|U|4927
*
4D5Y|1|2|G|4941
4D5Y|1|2|C|4942
4D5Y|1|2|U|4943
4D5Y|1|2|U|4944
4D5Y|1|2|C|4945
4D5Y|1|2|U|4946
4D5Y|1|2|G|4947
*
4D5Y|1|2|C|5014
4D5Y|1|2|A|5015
4D5Y|1|2|A|5016
4D5Y|1|2|G|5017

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain B

60S RIBOSOMAL PROTEIN UL3

Chain P

60S RIBOSOMAL PROTEIN UL22

Chain d

60S RIBOSOMAL PROTEIN EL31