J3_7SYN_006

3D structure

PDB id

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

Description

Structure of the HCV IRES bound to the 40S ribosomal subunit, head opening. Structure 8(delta dII)

Experimental method

ELECTRON MICROSCOPY

Resolution

4 Å

Loop

Sequence

CCAG*CCAGUAA*UGAUUAAG

Length

19 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_7SYN_006 not in the Motif Atlas

Homologous match to J3_8P9A_076

Geometric discrepancy: 0.2857

The information below is about J3_8P9A_076

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_85722.1

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

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

Current chains

Chain 2

18S rRNA

Nearby chains

Chain G

uS7

Chain R

uS9

Chain d

eS28