3D structure

PDB id
8T3D (explore in PDB, NAKB, or RNA 3D Hub)
Description
Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III
Experimental method
ELECTRON MICROSCOPY
Resolution
2.95 Å

Loop

Sequence
AGAAGACC*GGAUAACUG*CUU(5MC)GAUGUC*GGUUUAG*(PSU)AGUUU
Length
40 nucleotides
Bulged bases
8T3D|1|A1|A|2404, 8T3D|1|A1|A|2817, 8T3D|1|A1|U|2873, 8T3D|1|A1|U|2978, 8T3D|1|A1|U|2979
QA status
Modified nucleotides: 5MC, PSU

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

8T3D|1|A1|A|2399
8T3D|1|A1|G|2400
8T3D|1|A1|A|2401
8T3D|1|A1|A|2402
8T3D|1|A1|G|2403
8T3D|1|A1|A|2404
8T3D|1|A1|C|2405
8T3D|1|A1|C|2406
*
8T3D|1|A1|G|2815
8T3D|1|A1|G|2816
8T3D|1|A1|A|2817
8T3D|1|A1|U|2818
8T3D|1|A1|A|2819
8T3D|1|A1|A|2820
8T3D|1|A1|C|2821
8T3D|1|A1|U|2822
8T3D|1|A1|G|2823
*
8T3D|1|A1|C|2867
8T3D|1|A1|U|2868
8T3D|1|A1|U|2869
8T3D|1|A1|5MC|2870
8T3D|1|A1|G|2871
8T3D|1|A1|A|2872
8T3D|1|A1|U|2873
8T3D|1|A1|G|2874
8T3D|1|A1|U|2875
8T3D|1|A1|C|2876
*
8T3D|1|A1|G|2951
8T3D|1|A1|G|2952
8T3D|1|A1|U|2953
8T3D|1|A1|U|2954
8T3D|1|A1|U|2955
8T3D|1|A1|A|2956
8T3D|1|A1|G|2957
*
8T3D|1|A1|PSU|2975
8T3D|1|A1|A|2976
8T3D|1|A1|G|2977
8T3D|1|A1|U|2978
8T3D|1|A1|U|2979
8T3D|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
RPL4A isoform 1
Chain AI
60S ribosomal protein L10
Chain AP
60S ribosomal protein L17-A
Chain Aa
60S ribosomal protein L28
Chain Ab
RPL29 isoform 1

Coloring options:

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