Loop J5_9YDB

3D structure

PDB id: 9YDB (explore in PDB, NAKB, or RNA 3D Hub)
Description: Eukaryotic pre-60S ribosomes from uL16 P-site loop mutants in bypass condition. Lsg1,Nmd3 and Tif6 present
Experimental method: ELECTRON MICROSCOPY
Resolution: 2.83 Å

Loop

Sequence: AGAAGACC*GGAUAACUG*CUUCGAUGUC*GGUUUAG*UAGUUU
Length: 40 nucleotides
Bulged bases: 9YDB|1|A|A|2404, 9YDB|1|A|A|2817, 9YDB|1|A|U|2818, 9YDB|1|A|U|2978, 9YDB|1|A|U|2979
QA status: Valid loop

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

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

Current chains

Chain A: 25S RNA

Nearby chains

Chain LD: 60S ribosomal protein L2-A
Chain LE: 60S ribosomal protein L3
Chain LF: 60S ribosomal protein L4-A
Chain LR: 60S ribosomal protein L17-A
Chain Lc: 60S ribosomal protein L28
Chain Ld: 60S ribosomal protein L29
Chain V: 60S ribosomal export protein NMD3
Chain z: Cytoplasmic 60S subunit biogenesis factor REH1

J5_9YDB_005