J4_7SYJ_002

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

CAUUAAAUC*GCC*GUGAC*GG

Length

19 nucleotides

Bulged bases

7SYJ|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_7SYJ_002 not in the Motif Atlas

Homologous match to J4_8C3A_021

Geometric discrepancy: 0.2039

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

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

Current chains

Chain 2

18S rRNA

Nearby chains

Chain F

40S ribosomal protein S4

Chain J

eS8

Chain M

uS17

Chain Y

uS12