J3_7SYN_011

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

AGAUUAAG*CGCGCAAAU*AGU

Length

20 nucleotides

Bulged bases

7SYN|1|2|A|46

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_011 not in the Motif Atlas

Homologous match to J3_8P9A_069

Geometric discrepancy: 0.1274

The information below is about J3_8P9A_069

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_63856.1

Basepair signature

cWW-cWW-cSW-F-cWW-F-tHH-F-cWW-F-F-F-F

Number of instances in this motif group

5

Unit IDs

7SYN|1|2|A|40
7SYN|1|2|G|41
7SYN|1|2|A|42
7SYN|1|2|U|43
7SYN|1|2|U|44
7SYN|1|2|A|45
7SYN|1|2|A|46
7SYN|1|2|G|47
*
7SYN|1|2|C|479
7SYN|1|2|G|480
7SYN|1|2|C|481
7SYN|1|2|G|482
7SYN|1|2|C|483
7SYN|1|2|A|484
7SYN|1|2|A|485
7SYN|1|2|A|486
7SYN|1|2|U|487
*
7SYN|1|2|A|512
7SYN|1|2|G|513
7SYN|1|2|U|514

Current chains

Chain 2

18S rRNA

Nearby chains

Chain K

uS4

Chain Y

uS12