J4_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

GUGG*CGU*AAGAUUC*GC

Length

16 nucleotides

Bulged bases

6Q8Y|1|n|U|8, 6Q8Y|1|n|U|47, 6Q8Y|1|n|U|48

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

J4_6Q8Y_014 not in the Motif Atlas

Homologous match to J4_3TUP_001

Geometric discrepancy: 0.231

The information below is about J4_3TUP_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_58311.1

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

30

Unit IDs

6Q8Y|1|n|G|7
6Q8Y|1|n|U|8
6Q8Y|1|n|G|9
6Q8Y|1|n|G|10
*
6Q8Y|1|n|C|25
6Q8Y|1|n|G|26
6Q8Y|1|n|U|27
*
6Q8Y|1|n|A|43
6Q8Y|1|n|A|44
6Q8Y|1|n|G|45
6Q8Y|1|n|A|46
6Q8Y|1|n|U|47
6Q8Y|1|n|U|48
6Q8Y|1|n|C|49
*
6Q8Y|1|n|G|65
6Q8Y|1|n|C|66

Current chains

Chain n

P-site tRNA

Nearby chains

Chain BD

60S ribosomal protein L10

Chain BQ

Large subunit ribosomal RNA; LSU rRNA