IL_6Q8Y_033

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

GUGCCAG*CGGUAAUUC

Length

16 nucleotides

Bulged bases

6Q8Y|1|2|A|579, 6Q8Y|1|2|U|581, 6Q8Y|1|2|U|582

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_033 not in the Motif Atlas

Homologous match to IL_4V88_415

Geometric discrepancy: 0.0983

The information below is about IL_4V88_415

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_54177.1

Basepair signature

cWW-cSW-tWH-L-R-L-R-tHS-cWW

Number of instances in this motif group

5

Unit IDs

6Q8Y|1|2|G|562
6Q8Y|1|2|U|563
6Q8Y|1|2|G|564
6Q8Y|1|2|C|565
6Q8Y|1|2|C|566
6Q8Y|1|2|A|567
6Q8Y|1|2|G|568
*
6Q8Y|1|2|C|575
6Q8Y|1|2|G|576
6Q8Y|1|2|G|577
6Q8Y|1|2|U|578
6Q8Y|1|2|A|579
6Q8Y|1|2|A|580
6Q8Y|1|2|U|581
6Q8Y|1|2|U|582
6Q8Y|1|2|C|583

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain A

40S ribosomal protein S3

Chain c

40S ribosomal protein S23-A

Chain g

40S ribosomal protein S30-A