J5_6XIR_009

3D structure

PDB id

6XIR (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress

Experimental method

ELECTRON MICROSCOPY

Resolution

3.2 Å

Loop

Sequence

ACUUUGG*CUUUCCUUC*GGACUUU*AUAGAAUAGGACGUUUG*CAUCGUAAUGAU

Length

52 nucleotides

Bulged bases

6XIR|1|2|U|639, 6XIR|1|2|U|693, 6XIR|1|2|U|694, 6XIR|1|2|U|695, 6XIR|1|2|C|696, 6XIR|1|2|C|697, 6XIR|1|2|U|698, 6XIR|1|2|U|699, 6XIR|1|2|G|739, 6XIR|1|2|A|740, 6XIR|1|2|C|741, 6XIR|1|2|U|742, 6XIR|1|2|U|743, 6XIR|1|2|A|809, 6XIR|1|2|G|810, 6XIR|1|2|A|812, 6XIR|1|2|U|813, 6XIR|1|2|G|815, 6XIR|1|2|U|820, 6XIR|1|2|A|856, 6XIR|1|2|U|857

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

6XIR|1|2|A|636
6XIR|1|2|C|637
6XIR|1|2|U|638
6XIR|1|2|U|639
6XIR|1|2|U|640
6XIR|1|2|G|641
6XIR|1|2|G|642
*
6XIR|1|2|C|692
6XIR|1|2|U|693
6XIR|1|2|U|694
6XIR|1|2|U|695
6XIR|1|2|C|696
6XIR|1|2|C|697
6XIR|1|2|U|698
6XIR|1|2|U|699
6XIR|1|2|C|700
*
6XIR|1|2|G|738
6XIR|1|2|G|739
6XIR|1|2|A|740
6XIR|1|2|C|741
6XIR|1|2|U|742
6XIR|1|2|U|743
6XIR|1|2|U|744
*
6XIR|1|2|A|807
6XIR|1|2|U|808
6XIR|1|2|A|809
6XIR|1|2|G|810
6XIR|1|2|A|811
6XIR|1|2|A|812
6XIR|1|2|U|813
6XIR|1|2|A|814
6XIR|1|2|G|815
6XIR|1|2|G|816
6XIR|1|2|A|817
6XIR|1|2|C|818
6XIR|1|2|G|819
6XIR|1|2|U|820
6XIR|1|2|U|821
6XIR|1|2|U|822
6XIR|1|2|G|823
*
6XIR|1|2|C|849
6XIR|1|2|A|850
6XIR|1|2|U|851
6XIR|1|2|C|852
6XIR|1|2|G|853
6XIR|1|2|U|854
6XIR|1|2|A|855
6XIR|1|2|A|856
6XIR|1|2|U|857
6XIR|1|2|G|858
6XIR|1|2|A|859
6XIR|1|2|U|860

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain AB

40S ribosomal protein S11-A

Chain AD

40S ribosomal protein S13

Chain AM

RPS22A isoform 1

Chain R

60S ribosomal protein L19-A

Chain u

40S ribosomal protein S4-A

Chain x

40S ribosomal protein S7-A