J4_6XIR_011

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

AAG*CGAAAG*CCAUAAACUAUG*UU

Length

23 nucleotides

Bulged bases

6XIR|1|2|A|623, 6XIR|1|2|U|1024, 6XIR|1|2|A|1026, 6XIR|1|2|C|1028, 6XIR|1|2|U|1029, 6XIR|1|2|A|1030, 6XIR|1|2|U|1031

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_6XIR_011 not in the Motif Atlas

Homologous match to J4_8P9A_022

Geometric discrepancy: 0.5526

The information below is about J4_8P9A_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61885.6

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F

Number of instances in this motif group

4

Unit IDs

6XIR|1|2|A|622
6XIR|1|2|A|623
6XIR|1|2|G|624
*
6XIR|1|2|C|975
6XIR|1|2|G|976
6XIR|1|2|A|977
6XIR|1|2|A|978
6XIR|1|2|A|979
6XIR|1|2|G|980
*
6XIR|1|2|C|1021
6XIR|1|2|C|1022
6XIR|1|2|A|1023
6XIR|1|2|U|1024
6XIR|1|2|A|1025
6XIR|1|2|A|1026
6XIR|1|2|A|1027
6XIR|1|2|C|1028
6XIR|1|2|U|1029
6XIR|1|2|A|1030
6XIR|1|2|U|1031
6XIR|1|2|G|1032
*
6XIR|1|2|U|1103
6XIR|1|2|U|1104

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain 1

Large subunit ribosomal RNA; LSU rRNA

Chain AB

40S ribosomal protein S11-A

Chain AD

40S ribosomal protein S13

Chain AE

40S ribosomal protein S14-B

Chain AM

RPS22A isoform 1

Chain AN

40S ribosomal protein S23-A

Chain AQ

RPS26B isoform 1

Chain n

RPL41A isoform 1