J3_7SYK_018

3D structure

PDB id

7SYK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the HCV IRES binding to the 40S ribosomal subunit, closed conformation. Structure 5(delta dII)

Experimental method

ELECTRON MICROSCOPY

Resolution

4.2 Å

Loop

Sequence

CUUAAUUU*GGGAAACCUCAC*GGCUG

Length

25 nucleotides

Bulged bases

7SYK|1|2|G|1256, 7SYK|1|2|A|1258, 7SYK|1|2|A|1260

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_7SYK_018 not in the Motif Atlas

Homologous match to J3_8CRE_080

Geometric discrepancy: 0.1974

The information below is about J3_8CRE_080

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_83516.4

Basepair signature

cWW-tWW-F-F-F-F-F-tSS-cWW-F-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

4

Unit IDs

7SYK|1|2|C|1237
7SYK|1|2|U|1238
7SYK|1|2|U|1239
7SYK|1|2|A|1240
7SYK|1|2|A|1241
7SYK|1|2|U|1242
7SYK|1|2|U|1243
7SYK|1|2|U|1244
*
7SYK|1|2|G|1255
7SYK|1|2|G|1256
7SYK|1|2|G|1257
7SYK|1|2|A|1258
7SYK|1|2|A|1259
7SYK|1|2|A|1260
7SYK|1|2|C|1261
7SYK|1|2|C|1262
7SYK|1|2|U|1263
7SYK|1|2|C|1264
7SYK|1|2|A|1265
7SYK|1|2|C|1266
*
7SYK|1|2|G|1516
7SYK|1|2|G|1517
7SYK|1|2|C|1518
7SYK|1|2|U|1519
7SYK|1|2|G|1520

Current chains

Chain 2

18S rRNA

Nearby chains

Chain Q

uS19

Chain T

uS13

Chain V

uS10

Chain e

eS29