J3_6Q8Y_009

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

CCAGAC*GGGUG*UUAGACG

Length

18 nucleotides

Bulged bases

6Q8Y|1|2|A|1217, 6Q8Y|1|2|G|1445, 6Q8Y|1|2|C|1447

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

J3_6Q8Y_009 not in the Motif Atlas

Homologous match to J3_4V88_038

Geometric discrepancy: 0.1128

The information below is about J3_4V88_038

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_75993.1

Basepair signature

cWW-tWH-F-F-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

2

Unit IDs

6Q8Y|1|2|C|1215
6Q8Y|1|2|C|1216
6Q8Y|1|2|A|1217
6Q8Y|1|2|G|1218
6Q8Y|1|2|A|1219
6Q8Y|1|2|C|1220
*
6Q8Y|1|2|G|1263
6Q8Y|1|2|G|1264
6Q8Y|1|2|G|1265
6Q8Y|1|2|U|1266
6Q8Y|1|2|G|1267
*
6Q8Y|1|2|U|1442
6Q8Y|1|2|U|1443
6Q8Y|1|2|A|1444
6Q8Y|1|2|G|1445
6Q8Y|1|2|A|1446
6Q8Y|1|2|C|1447
6Q8Y|1|2|G|1448

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C

40S ribosomal protein S10-A

Chain M

40S ribosomal protein S29-A