Loop J5_9DP7

3D structure

PDB id: 9DP7 (explore in PDB, NAKB, or RNA 3D Hub)
Description: Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II
Experimental method: ELECTRON MICROSCOPY
Resolution: 2.38 Å

Loop

Sequence: AUAGUUCCUUUACUACAUGG*CAUGCUUAAAA*UG*CGA*UGGUU
Length: 41 nucleotides
Bulged bases: 9DP7|1|B5|C|130, 9DP7|1|B5|U|133, 9DP7|1|B5|U|134, 9DP7|1|B5|A|135, 9DP7|1|B5|C|136, 9DP7|1|B5|U|137, 9DP7|1|B5|A|140, 9DP7|1|B5|U|141
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

9DP7|1|B5|A|124
9DP7|1|B5|U|125
9DP7|1|B5|A|126
9DP7|1|B5|G|127
9DP7|1|B5|U|128
9DP7|1|B5|U|129
9DP7|1|B5|C|130
9DP7|1|B5|C|131
9DP7|1|B5|U|132
9DP7|1|B5|U|133
9DP7|1|B5|U|134
9DP7|1|B5|A|135
9DP7|1|B5|C|136
9DP7|1|B5|U|137
9DP7|1|B5|A|138
9DP7|1|B5|C|139
9DP7|1|B5|A|140
9DP7|1|B5|U|141
9DP7|1|B5|G|142
9DP7|1|B5|G|143
*
9DP7|1|B5|C|172
9DP7|1|B5|A|173
9DP7|1|B5|U|174
9DP7|1|B5|G|175
9DP7|1|B5|C|176
9DP7|1|B5|U|177
9DP7|1|B5|U|178
9DP7|1|B5|A|179
9DP7|1|B5|A|180
9DP7|1|B5|A|181
9DP7|1|B5|A|182
*
9DP7|1|B5|U|203
9DP7|1|B5|G|204
*
9DP7|1|B5|C|263
9DP7|1|B5|G|264
9DP7|1|B5|A|265
*
9DP7|1|B5|U|289
9DP7|1|B5|G|290
9DP7|1|B5|G|291
9DP7|1|B5|U|292
9DP7|1|B5|U|293

Current chains

Chain B5: 18S rRNA

Nearby chains

Chain BE: 40S ribosomal protein S4-A
Chain BG: 40S ribosomal protein S6-A
Chain BI: 40S ribosomal protein S8-A

J5_9DP7_009