J3_6Q8Y_040

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

AGACG*CC*GAAAAU

Length

13 nucleotides

Bulged bases

None detected

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_040 not in the Motif Atlas

Homologous match to J3_8P9A_058

Geometric discrepancy: 0.0827

The information below is about J3_8P9A_058

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_08594.1

Basepair signature

cWW-tSH-tHH-F-F-cWW-F-cWW

Number of instances in this motif group

6

Unit IDs

6Q8Y|1|BQ|A|1654
6Q8Y|1|BQ|G|1655
6Q8Y|1|BQ|A|1656
6Q8Y|1|BQ|C|1657
6Q8Y|1|BQ|G|1658
*
6Q8Y|1|BQ|C|1791
6Q8Y|1|BQ|C|1792
*
6Q8Y|1|BQ|G|1796
6Q8Y|1|BQ|A|1797
6Q8Y|1|BQ|A|1798
6Q8Y|1|BQ|A|1799
6Q8Y|1|BQ|A|1800
6Q8Y|1|BQ|U|1801

Current chains

Chain BQ

25S ribosomal RNA

Nearby chains

Chain AT

60S ribosomal protein L43-A

Chain AW

60S ribosomal protein L2-A

Chain BN

60S ribosomal protein L34-A