J4_7SYN_001

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

CAUUAAAUC*GCC*GUGAC*GG

Length

19 nucleotides

Bulged bases

7SYN|1|2|G|407

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

J4_7SYN_001 not in the Motif Atlas

Homologous match to J4_8C3A_021

Geometric discrepancy: 0.1568

The information below is about J4_8C3A_021

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_78231.1

Basepair signature

cWW-cSH-tHS-cWW-F-F-tHW-F-cWW-F-F-F-cWW

Number of instances in this motif group

2

Unit IDs

7SYN|1|2|C|98
7SYN|1|2|A|99
7SYN|1|2|U|100
7SYN|1|2|U|101
7SYN|1|2|A|102
7SYN|1|2|A|103
7SYN|1|2|A|104
7SYN|1|2|U|105
7SYN|1|2|C|106
*
7SYN|1|2|G|355
7SYN|1|2|C|356
7SYN|1|2|C|357
*
7SYN|1|2|G|405
7SYN|1|2|U|406
7SYN|1|2|G|407
7SYN|1|2|A|408
7SYN|1|2|C|409
*
7SYN|1|2|G|431
7SYN|1|2|G|432

Current chains

Chain 2

18S rRNA

Nearby chains

Chain F

eS4 (S4 X isoform)

Chain J

eS8

Chain M

uS17

Chain Y

uS12