J4_7SYO_002

3D structure

PDB id

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

Description

Structure of the HCV IRES bound to the 40S ribosomal subunit, head open. Structure 9(delta dII)

Experimental method

ELECTRON MICROSCOPY

Resolution

4.6 Å

Loop

Sequence

AAG*CGAAAG*CCAUAAACGAUG*UU

Length

23 nucleotides

Bulged bases

7SYO|1|2|A|672, 7SYO|1|2|A|1087

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_7SYO_002 not in the Motif Atlas

Homologous match to J4_8P9A_022

Geometric discrepancy: 0.1607

The information below is about J4_8P9A_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61885.6

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F

Number of instances in this motif group

4

Unit IDs

7SYO|1|2|A|671
7SYO|1|2|A|672
7SYO|1|2|G|673
*
7SYO|1|2|C|1032
7SYO|1|2|G|1033
7SYO|1|2|A|1034
7SYO|1|2|A|1035
7SYO|1|2|A|1036
7SYO|1|2|G|1037
*
7SYO|1|2|C|1078
7SYO|1|2|C|1079
7SYO|1|2|A|1080
7SYO|1|2|U|1081
7SYO|1|2|A|1082
7SYO|1|2|A|1083
7SYO|1|2|A|1084
7SYO|1|2|C|1085
7SYO|1|2|G|1086
7SYO|1|2|A|1087
7SYO|1|2|U|1088
7SYO|1|2|G|1089
*
7SYO|1|2|U|1160
7SYO|1|2|U|1161

Current chains

Chain 2

18S rRNA

Nearby chains

Chain M

uS17

Chain O

uS15

Chain X

uS8

Chain Y

uS12

Chain b

eS26

Chain n

eL41