J5_6Q8Y_008

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

CGAG*CGUAA*UGAACGUAG*CGA*UAAGAG

Length

27 nucleotides

Bulged bases

6Q8Y|1|BQ|U|719, 6Q8Y|1|BQ|A|784, 6Q8Y|1|BQ|G|785

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

J5_6Q8Y_008 not in the Motif Atlas

Homologous match to J5_8P9A_012

Geometric discrepancy: 0.081

The information below is about J5_8P9A_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_56629.1

Basepair signature

cWW-F-F-tSS-F-cWW-cWW-F-F-cWW-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

3

Unit IDs

6Q8Y|1|BQ|C|675
6Q8Y|1|BQ|G|676
6Q8Y|1|BQ|A|677
6Q8Y|1|BQ|G|678
*
6Q8Y|1|BQ|C|702
6Q8Y|1|BQ|G|703
6Q8Y|1|BQ|U|704
6Q8Y|1|BQ|A|705
6Q8Y|1|BQ|A|706
*
6Q8Y|1|BQ|U|713
6Q8Y|1|BQ|G|714
6Q8Y|1|BQ|A|715
6Q8Y|1|BQ|A|716
6Q8Y|1|BQ|C|717
6Q8Y|1|BQ|G|718
6Q8Y|1|BQ|U|719
6Q8Y|1|BQ|A|720
6Q8Y|1|BQ|G|721
*
6Q8Y|1|BQ|C|749
6Q8Y|1|BQ|G|750
6Q8Y|1|BQ|A|751
*
6Q8Y|1|BQ|U|782
6Q8Y|1|BQ|A|783
6Q8Y|1|BQ|A|784
6Q8Y|1|BQ|G|785
6Q8Y|1|BQ|A|786
6Q8Y|1|BQ|G|787

Current chains

Chain BQ

25S ribosomal RNA

Nearby chains

Chain AC

60S ribosomal protein L36-A

Chain AJ

60S ribosomal protein L13-A

Chain AR

60S ribosomal protein L28

Chain AV

60S ribosomal protein L29

Chain BB

60S ribosomal protein L18-A

Chain BE

60S ribosomal protein L4-A