J3_6IP8_020

3D structure

PDB id

6IP8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.9 Å

Loop

Sequence

AGAG*CAG*CUGGAU

Length

13 nucleotides

Bulged bases

None detected

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_6IP8_020 not in the Motif Atlas

Homologous match to J3_4V88_032

Geometric discrepancy: 0.2409

The information below is about J3_4V88_032

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_54972.1

Basepair signature

cWW-tWW-F-cWW-F-tHS-F-cWW

Number of instances in this motif group

2

Unit IDs

6IP8|1|2m|A|816
6IP8|1|2m|G|817
6IP8|1|2m|A|818
6IP8|1|2m|G|819
*
6IP8|1|2m|C|829
6IP8|1|2m|A|830
6IP8|1|2m|G|831
*
6IP8|1|2m|C|843
6IP8|1|2m|U|844
6IP8|1|2m|G|845
6IP8|1|2m|G|846
6IP8|1|2m|A|847
6IP8|1|2m|U|848

Current chains

Chain 2m

18S ribosomal RNA

Nearby chains

Chain 2q

40S ribosomal protein S4, X isoform

Chain 3I

40S ribosomal protein S9

Chain 3N

40S ribosomal protein S24