J5_8T3D_003

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

CGAG*CGUAA*UGAACGUAG*CGA*UAAGAG

Length

27 nucleotides

Bulged bases

8T3D|1|A1|U|719, 8T3D|1|A1|A|784, 8T3D|1|A1|G|785

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

J5_8T3D_003 not in the Motif Atlas

Homologous match to J5_8P9A_012

Geometric discrepancy: 0.0924

The information below is about J5_8P9A_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_23272.1

Basepair signature

cWW-F-F-F-F-cWW-cWW-F-F-F-cWW-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

2

Unit IDs

8T3D|1|A1|C|675
8T3D|1|A1|G|676
8T3D|1|A1|A|677
8T3D|1|A1|G|678
*
8T3D|1|A1|C|702
8T3D|1|A1|G|703
8T3D|1|A1|U|704
8T3D|1|A1|A|705
8T3D|1|A1|A|706
*
8T3D|1|A1|U|713
8T3D|1|A1|G|714
8T3D|1|A1|A|715
8T3D|1|A1|A|716
8T3D|1|A1|C|717
8T3D|1|A1|G|718
8T3D|1|A1|U|719
8T3D|1|A1|A|720
8T3D|1|A1|G|721
*
8T3D|1|A1|C|749
8T3D|1|A1|G|750
8T3D|1|A1|A|751
*
8T3D|1|A1|U|782
8T3D|1|A1|A|783
8T3D|1|A1|A|784
8T3D|1|A1|G|785
8T3D|1|A1|A|786
8T3D|1|A1|G|787

Current chains

Chain A1

25S rRNA

Nearby chains

Chain AC

RPL4A isoform 1

Chain AL

60S ribosomal protein L13-A

Chain AQ

60S ribosomal protein L18-A

Chain Aa

60S ribosomal protein L28

Chain Ab

RPL29 isoform 1

Chain Ai

60S ribosomal protein L36-A