J3_4D5Y_040

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

CUCCCACC*GGCG*CG

Length

14 nucleotides

Bulged bases

4D5Y|1|2|U|1082, 4D5Y|1|2|C|1083, 4D5Y|1|2|C|1084, 4D5Y|1|2|C|1085, 4D5Y|1|2|A|1086

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|1081
4D5Y|1|2|U|1082
4D5Y|1|2|C|1083
4D5Y|1|2|C|1084
4D5Y|1|2|C|1085
4D5Y|1|2|A|1086
4D5Y|1|2|C|1087
4D5Y|1|2|C|1088
*
4D5Y|1|2|G|1145
4D5Y|1|2|G|1146
4D5Y|1|2|C|1147
4D5Y|1|2|G|1148
*
4D5Y|1|2|C|1173
4D5Y|1|2|G|1174

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 4

5S ribosomal RNA; 5S rRNA

Chain D

60S RIBOSOMAL PROTEIN UL18

Chain S

60S RIBOSOMAL PROTEIN EL20

Chain T

60S RIBOSOMAL PROTEIN EL21