J5_6IP6_009

3D structure

PDB id

6IP6 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii)

Experimental method

ELECTRON MICROSCOPY

Resolution

4.5 Å

Loop

Sequence

GUCGCUCGCUCCUCUCCCACUU*AUGCCGACGGGC*GUGCAUU*ACCUCGGGCCGAU*ACGACCC

Length

61 nucleotides

Bulged bases

6IP6|1|2m|U|128, 6IP6|1|2m|C|129, 6IP6|1|2m|G|130, 6IP6|1|2m|C|131, 6IP6|1|2m|U|132, 6IP6|1|2m|C|133, 6IP6|1|2m|C|134, 6IP6|1|2m|U|135, 6IP6|1|2m|C|136, 6IP6|1|2m|U|137, 6IP6|1|2m|C|138, 6IP6|1|2m|C|139, 6IP6|1|2m|C|142, 6IP6|1|2m|U|143, 6IP6|1|2m|G|183, 6IP6|1|2m|U|305, 6IP6|1|2m|G|308

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

6IP6|1|2m|G|123
6IP6|1|2m|U|124
6IP6|1|2m|C|125
6IP6|1|2m|G|126
6IP6|1|2m|C|127
6IP6|1|2m|U|128
6IP6|1|2m|C|129
6IP6|1|2m|G|130
6IP6|1|2m|C|131
6IP6|1|2m|U|132
6IP6|1|2m|C|133
6IP6|1|2m|C|134
6IP6|1|2m|U|135
6IP6|1|2m|C|136
6IP6|1|2m|U|137
6IP6|1|2m|C|138
6IP6|1|2m|C|139
6IP6|1|2m|C|140
6IP6|1|2m|A|141
6IP6|1|2m|C|142
6IP6|1|2m|U|143
6IP6|1|2m|U|144
*
6IP6|1|2m|A|175
6IP6|1|2m|U|176
6IP6|1|2m|G|177
6IP6|1|2m|C|178
6IP6|1|2m|C|179
6IP6|1|2m|G|180
6IP6|1|2m|A|181
6IP6|1|2m|C|182
6IP6|1|2m|G|183
6IP6|1|2m|G|184
6IP6|1|2m|G|185
6IP6|1|2m|C|186
*
6IP6|1|2m|G|213
6IP6|1|2m|U|214
6IP6|1|2m|G|215
6IP6|1|2m|C|216
6IP6|1|2m|A|217
6IP6|1|2m|U|218
6IP6|1|2m|U|219
*
6IP6|1|2m|A|302
6IP6|1|2m|C|303
6IP6|1|2m|C|304
6IP6|1|2m|U|305
6IP6|1|2m|C|306
6IP6|1|2m|G|307
6IP6|1|2m|G|308
6IP6|1|2m|G|309
6IP6|1|2m|C|310
6IP6|1|2m|C|311
6IP6|1|2m|G|312
6IP6|1|2m|A|313
6IP6|1|2m|U|314
*
6IP6|1|2m|A|336
6IP6|1|2m|C|337
6IP6|1|2m|G|338
6IP6|1|2m|A|339
6IP6|1|2m|C|340
6IP6|1|2m|C|341
6IP6|1|2m|C|342

Current chains

Chain 2m

18S ribosomal RNA

Nearby chains

Chain 2Q

60S ribosomal protein L24

Chain 2q

40S ribosomal protein S4, X isoform

Chain 2t

40S ribosomal protein S8

Chain 3H

40S ribosomal protein S6