J3_7SYJ_006

3D structure

PDB id

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

Description

Structure of the HCV IRES binding to the 40S ribosomal subunit, closed conformation. Structure 4(delta dII)

Experimental method

ELECTRON MICROSCOPY

Resolution

4.8 Å

Loop

Sequence

CCAGG*CCCAGUAA*UGAUUAAG

Length

21 nucleotides

Bulged bases

None detected

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_7SYJ_006 not in the Motif Atlas

Homologous match to J3_8P9A_076

Geometric discrepancy: 0.572

The information below is about J3_8P9A_076

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_25303.4

Basepair signature

cWW-F-F-cSS-F-cWW-tWW-F-tWH-F-tHS-cSH-cWW

Number of instances in this motif group

4

Unit IDs

7SYJ|1|2|C|1218
7SYJ|1|2|C|1219
7SYJ|1|2|A|1220
7SYJ|1|2|G|1221
7SYJ|1|2|G|1222
*
7SYJ|1|2|C|1644
7SYJ|1|2|C|1645
7SYJ|1|2|C|1646
7SYJ|1|2|A|1647
7SYJ|1|2|G|1648
7SYJ|1|2|U|1649
7SYJ|1|2|A|1650
7SYJ|1|2|A|1651
*
7SYJ|1|2|U|1673
7SYJ|1|2|G|1674
7SYJ|1|2|A|1675
7SYJ|1|2|U|1676
7SYJ|1|2|U|1677
7SYJ|1|2|A|1678
7SYJ|1|2|A|1679
7SYJ|1|2|G|1680

Current chains

Chain 2

18S rRNA

Nearby chains

Chain G

uS7

Chain R

uS9

Chain d

eS28