J3_7SYN_009

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

CGGAC*GGGUG*UUAGAUG

Length

17 nucleotides

Bulged bases

7SYN|1|2|G|1274, 7SYN|1|2|G|1507, 7SYN|1|2|U|1509

QA status

Unknown status

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_009 not in the Motif Atlas

Homologous match to J3_8P9A_079

Geometric discrepancy: 0.5144

The information below is about J3_8P9A_079

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_87797.2

Basepair signature

cWW-tWH-F-F-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

3

Unit IDs

7SYN|1|2|C|1273
7SYN|1|2|G|1274
7SYN|1|2|G|1275
7SYN|1|2|A|1276
7SYN|1|2|C|1277
*
7SYN|1|2|G|1320
7SYN|1|2|G|1321
7SYN|1|2|G|1322
7SYN|1|2|U|1323
7SYN|1|2|G|1324
*
7SYN|1|2|U|1504
7SYN|1|2|U|1505
7SYN|1|2|A|1506
7SYN|1|2|G|1507
7SYN|1|2|A|1508
7SYN|1|2|U|1509
7SYN|1|2|G|1510

Current chains

Chain 2

18S rRNA

Nearby chains

Chain L

eS10

Chain e

uS14

Chain g

eS31