J5_6Q8Y_003

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*CGA*UGGUU

Length

41 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

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

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|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