J5_6IP8_008

3D structure

PDB id

6IP8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.9 Å

Loop

Sequence

GUCGCUCGCUCCUCUCCCACUU*AUGCCGACGGGC*GUGCAUU*ACCUCGGGCCGAU*ACGACCC

Length

61 nucleotides

Bulged bases

6IP8|1|2m|C|125, 6IP8|1|2m|U|128, 6IP8|1|2m|C|129, 6IP8|1|2m|G|130, 6IP8|1|2m|C|131, 6IP8|1|2m|U|132, 6IP8|1|2m|C|133, 6IP8|1|2m|C|134, 6IP8|1|2m|U|135, 6IP8|1|2m|C|136, 6IP8|1|2m|U|137, 6IP8|1|2m|C|138, 6IP8|1|2m|C|139, 6IP8|1|2m|C|142, 6IP8|1|2m|C|179, 6IP8|1|2m|G|183, 6IP8|1|2m|U|305, 6IP8|1|2m|C|306, 6IP8|1|2m|G|307, 6IP8|1|2m|G|308

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

6IP8|1|2m|G|123
6IP8|1|2m|U|124
6IP8|1|2m|C|125
6IP8|1|2m|G|126
6IP8|1|2m|C|127
6IP8|1|2m|U|128
6IP8|1|2m|C|129
6IP8|1|2m|G|130
6IP8|1|2m|C|131
6IP8|1|2m|U|132
6IP8|1|2m|C|133
6IP8|1|2m|C|134
6IP8|1|2m|U|135
6IP8|1|2m|C|136
6IP8|1|2m|U|137
6IP8|1|2m|C|138
6IP8|1|2m|C|139
6IP8|1|2m|C|140
6IP8|1|2m|A|141
6IP8|1|2m|C|142
6IP8|1|2m|U|143
6IP8|1|2m|U|144
*
6IP8|1|2m|A|175
6IP8|1|2m|U|176
6IP8|1|2m|G|177
6IP8|1|2m|C|178
6IP8|1|2m|C|179
6IP8|1|2m|G|180
6IP8|1|2m|A|181
6IP8|1|2m|C|182
6IP8|1|2m|G|183
6IP8|1|2m|G|184
6IP8|1|2m|G|185
6IP8|1|2m|C|186
*
6IP8|1|2m|G|213
6IP8|1|2m|U|214
6IP8|1|2m|G|215
6IP8|1|2m|C|216
6IP8|1|2m|A|217
6IP8|1|2m|U|218
6IP8|1|2m|U|219
*
6IP8|1|2m|A|302
6IP8|1|2m|C|303
6IP8|1|2m|C|304
6IP8|1|2m|U|305
6IP8|1|2m|C|306
6IP8|1|2m|G|307
6IP8|1|2m|G|308
6IP8|1|2m|G|309
6IP8|1|2m|C|310
6IP8|1|2m|C|311
6IP8|1|2m|G|312
6IP8|1|2m|A|313
6IP8|1|2m|U|314
*
6IP8|1|2m|A|336
6IP8|1|2m|C|337
6IP8|1|2m|G|338
6IP8|1|2m|A|339
6IP8|1|2m|C|340
6IP8|1|2m|C|341
6IP8|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