J5_4D67_001

3D structure

PDB id

4D67 (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

4D67|1|2|G|116, 4D67|1|2|G|119, 4D67|1|2|A|120, 4D67|1|2|G|148, 4D67|1|2|U|149, 4D67|1|2|A|155, 4D67|1|2|C|156, 4D67|1|2|C|300

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

4D67|1|2|C|111
4D67|1|2|C|112
4D67|1|2|A|113
4D67|1|2|G|114
4D67|1|2|C|115
4D67|1|2|G|116
4D67|1|2|C|117
4D67|1|2|C|118
4D67|1|2|G|119
4D67|1|2|A|120
4D67|1|2|A|121
4D67|1|2|U|122
4D67|1|2|C|123
4D67|1|2|C|124
4D67|1|2|C|125
*
4D67|1|2|G|143
4D67|1|2|A|144
4D67|1|2|C|145
4D67|1|2|A|146
4D67|1|2|U|147
4D67|1|2|G|148
4D67|1|2|U|149
4D67|1|2|G|150
4D67|1|2|G|151
4D67|1|2|C|152
4D67|1|2|G|153
4D67|1|2|U|154
4D67|1|2|A|155
4D67|1|2|C|156
4D67|1|2|G|157
*
4D67|1|2|C|266
4D67|1|2|C|267
4D67|1|2|G|268
4D67|1|2|G|269
4D67|1|2|A|270
4D67|1|2|G|271
4D67|1|2|U|272
4D67|1|2|C|273
4D67|1|2|G|274
*
4D67|1|2|C|295
4D67|1|2|A|296
4D67|1|2|A|297
4D67|1|2|A|298
4D67|1|2|G|299
4D67|1|2|C|300
4D67|1|2|G|301
*
4D67|1|2|U|318
4D67|1|2|A|319
4D67|1|2|A|320
4D67|1|2|G|321

Current chains

Chain 2

28S RRNA

Nearby chains

Chain 3

5.8S ribosomal RNA; 5.8S rRNA

Chain G

60S RIBOSOMAL PROTEIN L7A

Chain L

60S RIBOSOMAL PROTEIN L13

Chain N

60S RIBOSOMAL PROTEIN L15

Chain h

60S RIBOSOMAL PROTEIN L35

Chain i

60S RIBOSOMAL PROTEIN L36