3D structure

PDB id
8CDL (explore in PDB, NAKB, or RNA 3D Hub)
Description
80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex
Experimental method
ELECTRON MICROSCOPY
Resolution
2.72 Å

Loop

Sequence
AGAAGACC*(OMG)GAUAACUG*CUU(5MC)GAUGUC*GGUUUAG*UAGUUU
Length
40 nucleotides
Bulged bases
8CDL|1|AA|A|2404, 8CDL|1|AA|A|2817, 8CDL|1|AA|U|2873, 8CDL|1|AA|G|2874, 8CDL|1|AA|U|2978, 8CDL|1|AA|U|2979
QA status
Modified nucleotides: OMG, 5MC

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

8CDL|1|AA|A|2399
8CDL|1|AA|G|2400
8CDL|1|AA|A|2401
8CDL|1|AA|A|2402
8CDL|1|AA|G|2403
8CDL|1|AA|A|2404
8CDL|1|AA|C|2405
8CDL|1|AA|C|2406
*
8CDL|1|AA|OMG|2815
8CDL|1|AA|G|2816
8CDL|1|AA|A|2817
8CDL|1|AA|U|2818
8CDL|1|AA|A|2819
8CDL|1|AA|A|2820
8CDL|1|AA|C|2821
8CDL|1|AA|U|2822
8CDL|1|AA|G|2823
*
8CDL|1|AA|C|2867
8CDL|1|AA|U|2868
8CDL|1|AA|U|2869
8CDL|1|AA|5MC|2870
8CDL|1|AA|G|2871
8CDL|1|AA|A|2872
8CDL|1|AA|U|2873
8CDL|1|AA|G|2874
8CDL|1|AA|U|2875
8CDL|1|AA|C|2876
*
8CDL|1|AA|G|2951
8CDL|1|AA|G|2952
8CDL|1|AA|U|2953
8CDL|1|AA|U|2954
8CDL|1|AA|U|2955
8CDL|1|AA|A|2956
8CDL|1|AA|G|2957
*
8CDL|1|AA|U|2975
8CDL|1|AA|A|2976
8CDL|1|AA|G|2977
8CDL|1|AA|U|2978
8CDL|1|AA|U|2979
8CDL|1|AA|U|2980

Current chains

Chain AA
25S ribosomal RNA

Nearby chains

Chain Bb
Transfer RNA; tRNA
Chain EE
60S ribosomal protein L2-A
Chain FF
60S ribosomal protein L3
Chain GG
60S ribosomal protein L4-A
Chain M
60S ribosomal protein L28
Chain MM
60S ribosomal protein L10
Chain N
60S ribosomal protein L29
Chain Pp
dipeptide

Coloring options:

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