J5_6Q8Y_001

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

CUUGU*AAAUAAC*GGAAUG*CAAU*AUAG

Length

26 nucleotides

Bulged bases

6Q8Y|1|2|A|544

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

J5_6Q8Y_001 not in the Motif Atlas

Homologous match to J5_8C3A_018

Geometric discrepancy: 0.0819

The information below is about J5_8C3A_018

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_19320.1

Basepair signature

cWW-F-F-F-F-F-cWW-cWW-cWH-F-cWW-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

1

Unit IDs

6Q8Y|1|2|C|31
6Q8Y|1|2|U|32
6Q8Y|1|2|U|33
6Q8Y|1|2|G|34
6Q8Y|1|2|U|35
*
6Q8Y|1|2|A|473
6Q8Y|1|2|A|474
6Q8Y|1|2|A|475
6Q8Y|1|2|U|476
6Q8Y|1|2|A|477
6Q8Y|1|2|A|478
6Q8Y|1|2|C|479
*
6Q8Y|1|2|G|509
6Q8Y|1|2|G|510
6Q8Y|1|2|A|511
6Q8Y|1|2|A|512
6Q8Y|1|2|U|513
6Q8Y|1|2|G|514
*
6Q8Y|1|2|C|543
6Q8Y|1|2|A|544
6Q8Y|1|2|A|545
6Q8Y|1|2|U|546
*
6Q8Y|1|2|A|592
6Q8Y|1|2|U|593
6Q8Y|1|2|A|594
6Q8Y|1|2|G|595

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain W

40S ribosomal protein S9-A

Chain c

40S ribosomal protein S23-A

Chain g

40S ribosomal protein S30-A