J3_4D5Y_033

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

CGGUUG*CCUUCG*CGCACCGCACGUUCGUG

Length

29 nucleotides

Bulged bases

4D5Y|1|2|U|4711, 4D5Y|1|2|U|4712, 4D5Y|1|2|U|4837, 4D5Y|1|2|A|4893, 4D5Y|1|2|C|4894, 4D5Y|1|2|C|4895, 4D5Y|1|2|G|4896, 4D5Y|1|2|C|4897, 4D5Y|1|2|G|4900, 4D5Y|1|2|U|4901, 4D5Y|1|2|U|4902, 4D5Y|1|2|C|4903

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

4D5Y|1|2|C|4708
4D5Y|1|2|G|4709
4D5Y|1|2|G|4710
4D5Y|1|2|U|4711
4D5Y|1|2|U|4712
4D5Y|1|2|G|4713
*
4D5Y|1|2|C|4834
4D5Y|1|2|C|4835
4D5Y|1|2|U|4836
4D5Y|1|2|U|4837
4D5Y|1|2|C|4838
4D5Y|1|2|G|4839
*
4D5Y|1|2|C|4890
4D5Y|1|2|G|4891
4D5Y|1|2|C|4892
4D5Y|1|2|A|4893
4D5Y|1|2|C|4894
4D5Y|1|2|C|4895
4D5Y|1|2|G|4896
4D5Y|1|2|C|4897
4D5Y|1|2|A|4898
4D5Y|1|2|C|4899
4D5Y|1|2|G|4900
4D5Y|1|2|U|4901
4D5Y|1|2|U|4902
4D5Y|1|2|C|4903
4D5Y|1|2|G|4904
4D5Y|1|2|U|4905
4D5Y|1|2|G|4906

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain E

60S RIBOSOMAL PROTEIN EL6

Chain M

60S RIBOSOMAL PROTEIN EL14

Chain O

60S RIBOSOMAL PROTEIN UL13

Chain f

60S RIBOSOMAL PROTEIN EL33