J3_6Q8Y_013

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

CACUG*CGUGCUGGGGAUA*UUCAGCGAG

Length

27 nucleotides

Bulged bases

6Q8Y|1|2|U|1473, 6Q8Y|1|2|G|1539, 6Q8Y|1|2|G|1572

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|C|1470
6Q8Y|1|2|A|1471
6Q8Y|1|2|C|1472
6Q8Y|1|2|U|1473
6Q8Y|1|2|G|1474
*
6Q8Y|1|2|C|1533
6Q8Y|1|2|G|1534
6Q8Y|1|2|U|1535
6Q8Y|1|2|G|1536
6Q8Y|1|2|C|1537
6Q8Y|1|2|U|1538
6Q8Y|1|2|G|1539
6Q8Y|1|2|G|1540
6Q8Y|1|2|G|1541
6Q8Y|1|2|G|1542
6Q8Y|1|2|A|1543
6Q8Y|1|2|U|1544
6Q8Y|1|2|A|1545
*
6Q8Y|1|2|U|1566
6Q8Y|1|2|U|1567
6Q8Y|1|2|C|1568
6Q8Y|1|2|A|1569
6Q8Y|1|2|G|1570
6Q8Y|1|2|C|1571
6Q8Y|1|2|G|1572
6Q8Y|1|2|A|1573
6Q8Y|1|2|G|1574

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain B

Rps5p

Chain H

40S ribosomal protein S18-A

Chain I

40S ribosomal protein S19-A

Chain K

40S ribosomal protein S25-A