J4_6Q8Y_004

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

CUAUG*CGUC*GAG*CGUGUG

Length

18 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

J4_6Q8Y_004 not in the Motif Atlas

Homologous match to J4_8P9A_013

Geometric discrepancy: 0.1122

The information below is about J4_8P9A_013

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_43318.1

Basepair signature

cWW-cWW-F-F-cSS-F-cWW-tHS-cWW-F-cWW

Number of instances in this motif group

2

Unit IDs

6Q8Y|1|BQ|C|185
6Q8Y|1|BQ|U|186
6Q8Y|1|BQ|A|187
6Q8Y|1|BQ|U|188
6Q8Y|1|BQ|G|189
*
6Q8Y|1|BQ|C|205
6Q8Y|1|BQ|G|206
6Q8Y|1|BQ|U|207
6Q8Y|1|BQ|C|208
*
6Q8Y|1|BQ|G|212
6Q8Y|1|BQ|A|213
6Q8Y|1|BQ|G|214
*
6Q8Y|1|BQ|C|226
6Q8Y|1|BQ|G|227
6Q8Y|1|BQ|U|228
6Q8Y|1|BQ|G|229
6Q8Y|1|BQ|U|230
6Q8Y|1|BQ|G|231

Current chains

Chain BQ

25S ribosomal RNA

Nearby chains

Chain AK

60S ribosomal protein L26-A

Chain BE

60S ribosomal protein L4-A

Chain BS

5.8S ribosomal RNA; 5.8S rRNA