J3_5IT9_008

3D structure

PDB id

5IT9 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.

Experimental method

ELECTRON MICROSCOPY

Resolution

3.8 Å

Loop

Sequence

CUUAAUUU*GGGGAAACUCAC*GGCCG

Length

25 nucleotides

Bulged bases

5IT9|1|2|G|1198, 5IT9|1|2|G|1200, 5IT9|1|2|A|1202

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

J3_5IT9_008 not in the Motif Atlas

Geometric match to J3_8C3A_040

Geometric discrepancy: 0.1889

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

5IT9|1|2|C|1179
5IT9|1|2|U|1180
5IT9|1|2|U|1181
5IT9|1|2|A|1182
5IT9|1|2|A|1183
5IT9|1|2|U|1184
5IT9|1|2|U|1185
5IT9|1|2|U|1186
*
5IT9|1|2|G|1197
5IT9|1|2|G|1198
5IT9|1|2|G|1199
5IT9|1|2|G|1200
5IT9|1|2|A|1201
5IT9|1|2|A|1202
5IT9|1|2|A|1203
5IT9|1|2|C|1204
5IT9|1|2|U|1205
5IT9|1|2|C|1206
5IT9|1|2|A|1207
5IT9|1|2|C|1208
*
5IT9|1|2|G|1452
5IT9|1|2|G|1453
5IT9|1|2|C|1454
5IT9|1|2|C|1455
5IT9|1|2|G|1456

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain P

Ribosomal protein uS19

Chain S

Ribosomal protein uS13

Chain U

Ribosomal protein uS10

Chain d

Ribosomal protein eS29

Chain f

Ribosomal protein eS31

Chain i

Cripavirus internal ribosome entry site (IRES); CrPV IRES