IL_6Q8Y_014

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

GUA*UUUUC

Length

8 nucleotides

Bulged bases

6Q8Y|1|2|U|260

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

IL_6Q8Y_014 not in the Motif Atlas

Homologous match to IL_4V88_397

Geometric discrepancy: 0.2551

The information below is about IL_4V88_397

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

Major groove platform

Motif group

IL_63959.1

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

18

Unit IDs

6Q8Y|1|2|G|204
6Q8Y|1|2|U|205
6Q8Y|1|2|A|206
*
6Q8Y|1|2|U|259
6Q8Y|1|2|U|260
6Q8Y|1|2|U|261
6Q8Y|1|2|U|262
6Q8Y|1|2|C|263

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain S

40S ribosomal protein S4-A

Chain V

40S ribosomal protein S8-A