J3_8T3D_038

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

C(PSU)UAAUU(PSU)*GGGGAAACUCAC*GGCCG

Length

25 nucleotides

Bulged bases

8T3D|1|B5|G|1199, 8T3D|1|B5|G|1201, 8T3D|1|B5|A|1203

QA status

Modified nucleotides: 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

J3_8T3D_038 not in the Motif Atlas

Homologous match to J3_8C3A_040

Geometric discrepancy: 0.0948

The information below is about J3_8C3A_040

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_83516.3

Basepair signature

cWW-F-F-F-tWW-F-tSH-tSS-cSS-F-F-F-F-F-cWW-cWW-F-F-F

Number of instances in this motif group

4

Unit IDs

8T3D|1|B5|C|1180
8T3D|1|B5|PSU|1181
8T3D|1|B5|U|1182
8T3D|1|B5|A|1183
8T3D|1|B5|A|1184
8T3D|1|B5|U|1185
8T3D|1|B5|U|1186
8T3D|1|B5|PSU|1187
*
8T3D|1|B5|G|1198
8T3D|1|B5|G|1199
8T3D|1|B5|G|1200
8T3D|1|B5|G|1201
8T3D|1|B5|A|1202
8T3D|1|B5|A|1203
8T3D|1|B5|A|1204
8T3D|1|B5|C|1205
8T3D|1|B5|U|1206
8T3D|1|B5|C|1207
8T3D|1|B5|A|1208
8T3D|1|B5|C|1209
*
8T3D|1|B5|G|1454
8T3D|1|B5|G|1455
8T3D|1|B5|C|1456
8T3D|1|B5|C|1457
8T3D|1|B5|G|1458

Current chains

Chain B5

18S rRNA

Nearby chains

Chain BP

RPS15 isoform 1

Chain BS

40S ribosomal protein S18-A

Chain BU

RPS20 isoform 1

Chain Bd

RPS29A isoform 1

Chain Bf

Ubiquitin-40S ribosomal protein S31