J5_4D5Y_001

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

CCAGCGCCGAAUCCC*GACAUGUGGCGUACG*CCGGAGUCG*CAAAGCG*UAAG

Length

50 nucleotides

Bulged bases

4D5Y|1|2|G|116, 4D5Y|1|2|G|119, 4D5Y|1|2|A|120, 4D5Y|1|2|G|148, 4D5Y|1|2|U|149, 4D5Y|1|2|A|155, 4D5Y|1|2|C|156, 4D5Y|1|2|C|300

QA status

Unknown status

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|111
4D5Y|1|2|C|112
4D5Y|1|2|A|113
4D5Y|1|2|G|114
4D5Y|1|2|C|115
4D5Y|1|2|G|116
4D5Y|1|2|C|117
4D5Y|1|2|C|118
4D5Y|1|2|G|119
4D5Y|1|2|A|120
4D5Y|1|2|A|121
4D5Y|1|2|U|122
4D5Y|1|2|C|123
4D5Y|1|2|C|124
4D5Y|1|2|C|125
*
4D5Y|1|2|G|143
4D5Y|1|2|A|144
4D5Y|1|2|C|145
4D5Y|1|2|A|146
4D5Y|1|2|U|147
4D5Y|1|2|G|148
4D5Y|1|2|U|149
4D5Y|1|2|G|150
4D5Y|1|2|G|151
4D5Y|1|2|C|152
4D5Y|1|2|G|153
4D5Y|1|2|U|154
4D5Y|1|2|A|155
4D5Y|1|2|C|156
4D5Y|1|2|G|157
*
4D5Y|1|2|C|266
4D5Y|1|2|C|267
4D5Y|1|2|G|268
4D5Y|1|2|G|269
4D5Y|1|2|A|270
4D5Y|1|2|G|271
4D5Y|1|2|U|272
4D5Y|1|2|C|273
4D5Y|1|2|G|274
*
4D5Y|1|2|C|295
4D5Y|1|2|A|296
4D5Y|1|2|A|297
4D5Y|1|2|A|298
4D5Y|1|2|G|299
4D5Y|1|2|C|300
4D5Y|1|2|G|301
*
4D5Y|1|2|U|318
4D5Y|1|2|A|319
4D5Y|1|2|A|320
4D5Y|1|2|G|321

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 3

5.8S ribosomal RNA; 5.8S rRNA

Chain G

60S RIBOSOMAL PROTEIN EL8

Chain L

60S RIBOSOMAL PROTEIN EL13

Chain N

60S RIBOSOMAL PROTEIN EL15

Chain h

60S RIBOSOMAL PROTEIN UL29

Chain i

60S RIBOSOMAL PROTEIN EL36