J5_6XIR_005

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

AGAAGACC*GGAUAACUG*CUUCGAUGUC*GGUUUAG*UAGUUU

Length

40 nucleotides

Bulged bases

6XIR|1|1|A|2404, 6XIR|1|1|A|2817, 6XIR|1|1|U|2873, 6XIR|1|1|G|2874, 6XIR|1|1|U|2978, 6XIR|1|1|U|2979

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|1|A|2399
6XIR|1|1|G|2400
6XIR|1|1|A|2401
6XIR|1|1|A|2402
6XIR|1|1|G|2403
6XIR|1|1|A|2404
6XIR|1|1|C|2405
6XIR|1|1|C|2406
*
6XIR|1|1|G|2815
6XIR|1|1|G|2816
6XIR|1|1|A|2817
6XIR|1|1|U|2818
6XIR|1|1|A|2819
6XIR|1|1|A|2820
6XIR|1|1|C|2821
6XIR|1|1|U|2822
6XIR|1|1|G|2823
*
6XIR|1|1|C|2867
6XIR|1|1|U|2868
6XIR|1|1|U|2869
6XIR|1|1|C|2870
6XIR|1|1|G|2871
6XIR|1|1|A|2872
6XIR|1|1|U|2873
6XIR|1|1|G|2874
6XIR|1|1|U|2875
6XIR|1|1|C|2876
*
6XIR|1|1|G|2951
6XIR|1|1|G|2952
6XIR|1|1|U|2953
6XIR|1|1|U|2954
6XIR|1|1|U|2955
6XIR|1|1|A|2956
6XIR|1|1|G|2957
*
6XIR|1|1|U|2975
6XIR|1|1|A|2976
6XIR|1|1|G|2977
6XIR|1|1|U|2978
6XIR|1|1|U|2979
6XIR|1|1|U|2980

Current chains

Chain 1

35S ribosomal RNA

Nearby chains

Chain A

60S ribosomal protein L2-A

Chain B

RPL3 isoform 1

Chain C

RPL4A isoform 1

Chain a

60S ribosomal protein L28

Chain b

RPL29 isoform 1