Loop J5_9DOV

3D structure

PDB id: 9DOV (explore in PDB, NAKB, or RNA 3D Hub)
Description: Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B
Experimental method: ELECTRON MICROSCOPY
Resolution: 2.49 Å

Loop

Sequence: AGAAGACC*(OMG)GAUAACUG*CUU(5MC)GAUGUC*GGUUUAG*UAGUUU
Length: 40 nucleotides
Bulged bases: 9DOV|1|A1|A|2404, 9DOV|1|A1|A|2817, 9DOV|1|A1|U|2873, 9DOV|1|A1|G|2874, 9DOV|1|A1|U|2978, 9DOV|1|A1|U|2979
QA status: Modified nucleotides: OMG, 5MC

Sequence variability

R3DSVS

Structural variability across Equivalence Class

R3DMCS EC

Structural variability across Rfam

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

9DOV|1|A1|A|2399
9DOV|1|A1|G|2400
9DOV|1|A1|A|2401
9DOV|1|A1|A|2402
9DOV|1|A1|G|2403
9DOV|1|A1|A|2404
9DOV|1|A1|C|2405
9DOV|1|A1|C|2406
*
9DOV|1|A1|OMG|2815
9DOV|1|A1|G|2816
9DOV|1|A1|A|2817
9DOV|1|A1|U|2818
9DOV|1|A1|A|2819
9DOV|1|A1|A|2820
9DOV|1|A1|C|2821
9DOV|1|A1|U|2822
9DOV|1|A1|G|2823
*
9DOV|1|A1|C|2867
9DOV|1|A1|U|2868
9DOV|1|A1|U|2869
9DOV|1|A1|5MC|2870
9DOV|1|A1|G|2871
9DOV|1|A1|A|2872
9DOV|1|A1|U|2873
9DOV|1|A1|G|2874
9DOV|1|A1|U|2875
9DOV|1|A1|C|2876
*
9DOV|1|A1|G|2951
9DOV|1|A1|G|2952
9DOV|1|A1|U|2953
9DOV|1|A1|U|2954
9DOV|1|A1|U|2955
9DOV|1|A1|A|2956
9DOV|1|A1|G|2957
*
9DOV|1|A1|U|2975
9DOV|1|A1|A|2976
9DOV|1|A1|G|2977
9DOV|1|A1|U|2978
9DOV|1|A1|U|2979
9DOV|1|A1|U|2980

Current chains

Chain A1: 25S rRNA

Nearby chains

Chain AA: 60S ribosomal protein L2-A
Chain AB: 60S ribosomal protein L3
Chain AC: Large ribosomal subunit protein uL4A
Chain Ab: Large ribosomal subunit protein eL29

J5_9DOV_005