Loop J5_6Q8Y

3D structure

PDB id: 6Q8Y (explore in PDB, NAKB, or RNA 3D Hub)
Description: Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex
Experimental method: ELECTRON MICROSCOPY
Resolution: 3.1 Å

Loop

Sequence: AUAGUUCCUUUACUACAUGG*CAUGCUUAAAA*UG*CGAAU*AUGGUU
Length: 44 nucleotides
Bulged bases: 6Q8Y|1|2|U|128, 6Q8Y|1|2|C|131, 6Q8Y|1|2|U|132, 6Q8Y|1|2|U|133, 6Q8Y|1|2|U|134, 6Q8Y|1|2|A|135, 6Q8Y|1|2|A|140, 6Q8Y|1|2|U|141, 6Q8Y|1|2|U|178
QA status: Valid loop

Sequence variability

R3DSVS

Structural variability across Equivalence Class

R3DMCS EC

Structural variability across Rfam

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

6Q8Y|1|2|A|124
6Q8Y|1|2|U|125
6Q8Y|1|2|A|126
6Q8Y|1|2|G|127
6Q8Y|1|2|U|128
6Q8Y|1|2|U|129
6Q8Y|1|2|C|130
6Q8Y|1|2|C|131
6Q8Y|1|2|U|132
6Q8Y|1|2|U|133
6Q8Y|1|2|U|134
6Q8Y|1|2|A|135
6Q8Y|1|2|C|136
6Q8Y|1|2|U|137
6Q8Y|1|2|A|138
6Q8Y|1|2|C|139
6Q8Y|1|2|A|140
6Q8Y|1|2|U|141
6Q8Y|1|2|G|142
6Q8Y|1|2|G|143
*
6Q8Y|1|2|C|172
6Q8Y|1|2|A|173
6Q8Y|1|2|U|174
6Q8Y|1|2|G|175
6Q8Y|1|2|C|176
6Q8Y|1|2|U|177
6Q8Y|1|2|U|178
6Q8Y|1|2|A|179
6Q8Y|1|2|A|180
6Q8Y|1|2|A|181
6Q8Y|1|2|A|182
*
6Q8Y|1|2|U|203
6Q8Y|1|2|G|204
*
6Q8Y|1|2|C|263
6Q8Y|1|2|G|264
6Q8Y|1|2|A|265
6Q8Y|1|2|A|266
6Q8Y|1|2|U|267
*
6Q8Y|1|2|A|288
6Q8Y|1|2|U|289
6Q8Y|1|2|G|290
6Q8Y|1|2|G|291
6Q8Y|1|2|U|292
6Q8Y|1|2|U|293

Current chains

Chain 2: 18S ribosomal RNA

Nearby chains

Chain S: 40S ribosomal protein S4-A
Chain T: 40S ribosomal protein S6-A
Chain V: 40S ribosomal protein S8-A

J5_6Q8Y_004