J5_6XIR_008

3D structure

PDB id

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

Description

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress

Experimental method

ELECTRON MICROSCOPY

Resolution

3.2 Å

Loop

Sequence

GAUAGUUCCUUUACUACAUGG*CAUGCUUAAAAUC*GAUG*CGAAU*AUGGUUC

Length

50 nucleotides

Bulged bases

6XIR|1|2|C|130, 6XIR|1|2|C|131, 6XIR|1|2|U|132, 6XIR|1|2|A|135, 6XIR|1|2|U|137, 6XIR|1|2|A|140, 6XIR|1|2|U|141, 6XIR|1|2|U|178, 6XIR|1|2|A|179, 6XIR|1|2|A|202, 6XIR|1|2|U|203

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

6XIR|1|2|G|123
6XIR|1|2|A|124
6XIR|1|2|U|125
6XIR|1|2|A|126
6XIR|1|2|G|127
6XIR|1|2|U|128
6XIR|1|2|U|129
6XIR|1|2|C|130
6XIR|1|2|C|131
6XIR|1|2|U|132
6XIR|1|2|U|133
6XIR|1|2|U|134
6XIR|1|2|A|135
6XIR|1|2|C|136
6XIR|1|2|U|137
6XIR|1|2|A|138
6XIR|1|2|C|139
6XIR|1|2|A|140
6XIR|1|2|U|141
6XIR|1|2|G|142
6XIR|1|2|G|143
*
6XIR|1|2|C|172
6XIR|1|2|A|173
6XIR|1|2|U|174
6XIR|1|2|G|175
6XIR|1|2|C|176
6XIR|1|2|U|177
6XIR|1|2|U|178
6XIR|1|2|A|179
6XIR|1|2|A|180
6XIR|1|2|A|181
6XIR|1|2|A|182
6XIR|1|2|U|183
6XIR|1|2|C|184
*
6XIR|1|2|G|201
6XIR|1|2|A|202
6XIR|1|2|U|203
6XIR|1|2|G|204
*
6XIR|1|2|C|263
6XIR|1|2|G|264
6XIR|1|2|A|265
6XIR|1|2|A|266
6XIR|1|2|U|267
*
6XIR|1|2|A|288
6XIR|1|2|U|289
6XIR|1|2|G|290
6XIR|1|2|G|291
6XIR|1|2|U|292
6XIR|1|2|U|293
6XIR|1|2|C|294

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain u

40S ribosomal protein S4-A

Chain w

40S ribosomal protein S6-A