J5_6Q8Y_005

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

ACUUUG*UUUCCU*ACUUU*AUAGAAUAGGA*UAAUGAU

Length

35 nucleotides

Bulged bases

6Q8Y|1|2|U|639, 6Q8Y|1|2|U|694, 6Q8Y|1|2|C|696, 6Q8Y|1|2|C|697, 6Q8Y|1|2|U|813, 6Q8Y|1|2|G|815, 6Q8Y|1|2|A|856

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

6Q8Y|1|2|A|636
6Q8Y|1|2|C|637
6Q8Y|1|2|U|638
6Q8Y|1|2|U|639
6Q8Y|1|2|U|640
6Q8Y|1|2|G|641
*
6Q8Y|1|2|U|693
6Q8Y|1|2|U|694
6Q8Y|1|2|U|695
6Q8Y|1|2|C|696
6Q8Y|1|2|C|697
6Q8Y|1|2|U|698
*
6Q8Y|1|2|A|740
6Q8Y|1|2|C|741
6Q8Y|1|2|U|742
6Q8Y|1|2|U|743
6Q8Y|1|2|U|744
*
6Q8Y|1|2|A|807
6Q8Y|1|2|U|808
6Q8Y|1|2|A|809
6Q8Y|1|2|G|810
6Q8Y|1|2|A|811
6Q8Y|1|2|A|812
6Q8Y|1|2|U|813
6Q8Y|1|2|A|814
6Q8Y|1|2|G|815
6Q8Y|1|2|G|816
6Q8Y|1|2|A|817
*
6Q8Y|1|2|U|854
6Q8Y|1|2|A|855
6Q8Y|1|2|A|856
6Q8Y|1|2|U|857
6Q8Y|1|2|G|858
6Q8Y|1|2|A|859
6Q8Y|1|2|U|860

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain BF

60S ribosomal protein L19-A

Chain U

40S ribosomal protein S7-A

Chain X

40S ribosomal protein S11-A

Chain Y

40S ribosomal protein S13

Chain b

40S ribosomal protein S22-A