J6_6XIR_004

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

CUUGUCUCAAAGAUUAAG*CGCGCAAAU*AGUGACAAUAAAUAAC*GGAAUG*CAAUU*AAUAG

Length

59 nucleotides

Bulged bases

6XIR|1|2|G|34, 6XIR|1|2|A|43, 6XIR|1|2|U|44, 6XIR|1|2|A|46, 6XIR|1|2|A|47, 6XIR|1|2|A|438, 6XIR|1|2|C|469, 6XIR|1|2|A|474, 6XIR|1|2|U|513, 6XIR|1|2|A|544, 6XIR|1|2|A|594

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|C|31
6XIR|1|2|U|32
6XIR|1|2|U|33
6XIR|1|2|G|34
6XIR|1|2|U|35
6XIR|1|2|C|36
6XIR|1|2|U|37
6XIR|1|2|C|38
6XIR|1|2|A|39
6XIR|1|2|A|40
6XIR|1|2|A|41
6XIR|1|2|G|42
6XIR|1|2|A|43
6XIR|1|2|U|44
6XIR|1|2|U|45
6XIR|1|2|A|46
6XIR|1|2|A|47
6XIR|1|2|G|48
*
6XIR|1|2|C|431
6XIR|1|2|G|432
6XIR|1|2|C|433
6XIR|1|2|G|434
6XIR|1|2|C|435
6XIR|1|2|A|436
6XIR|1|2|A|437
6XIR|1|2|A|438
6XIR|1|2|U|439
*
6XIR|1|2|A|464
6XIR|1|2|G|465
6XIR|1|2|U|466
6XIR|1|2|G|467
6XIR|1|2|A|468
6XIR|1|2|C|469
6XIR|1|2|A|470
6XIR|1|2|A|471
6XIR|1|2|U|472
6XIR|1|2|A|473
6XIR|1|2|A|474
6XIR|1|2|A|475
6XIR|1|2|U|476
6XIR|1|2|A|477
6XIR|1|2|A|478
6XIR|1|2|C|479
*
6XIR|1|2|G|509
6XIR|1|2|G|510
6XIR|1|2|A|511
6XIR|1|2|A|512
6XIR|1|2|U|513
6XIR|1|2|G|514
*
6XIR|1|2|C|543
6XIR|1|2|A|544
6XIR|1|2|A|545
6XIR|1|2|U|546
6XIR|1|2|U|547
*
6XIR|1|2|A|591
6XIR|1|2|A|592
6XIR|1|2|U|593
6XIR|1|2|A|594
6XIR|1|2|G|595

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain AN

40S ribosomal protein S23-A

Chain AO

40S ribosomal protein S24-A

Chain u

40S ribosomal protein S4-A

Chain z

40S ribosomal protein S9-A