J4_6Q8Y_005

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

CAAAUAU*AG*UGAU*AG

Length

15 nucleotides

Bulged bases

6Q8Y|1|BQ|A|1452, 6Q8Y|1|BQ|U|1455, 6Q8Y|1|BQ|A|1456

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

J4_6Q8Y_005 not in the Motif Atlas

Homologous match to J4_8P9A_014

Geometric discrepancy: 0.099

The information below is about J4_8P9A_014

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_34212.1

Basepair signature

cWW-F-cWW-F-F-F-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

6Q8Y|1|BQ|C|1451
6Q8Y|1|BQ|A|1452
6Q8Y|1|BQ|A|1453
6Q8Y|1|BQ|A|1454
6Q8Y|1|BQ|U|1455
6Q8Y|1|BQ|A|1456
6Q8Y|1|BQ|U|1457
*
6Q8Y|1|BQ|A|1475
6Q8Y|1|BQ|G|1476
*
6Q8Y|1|BQ|U|1877
6Q8Y|1|BQ|G|1878
6Q8Y|1|BQ|A|1879
6Q8Y|1|BQ|U|1880
*
6Q8Y|1|BQ|A|2352
6Q8Y|1|BQ|G|2353

Current chains

Chain BQ

25S ribosomal RNA

Nearby chains

Chain AX

60S ribosomal protein L17-A

Chain BC

60S ribosomal protein L31-A

Chain BF

60S ribosomal protein L19-A