HL_6IP8_035

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

AGCAGUU

Length

7 nucleotides

Bulged bases

6IP8|1|1A|G|2421, 6IP8|1|1A|U|2425

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

HL_6IP8_035 not in the Motif Atlas

Homologous match to HL_8C3A_032

Geometric discrepancy: 0.2083

The information below is about HL_8C3A_032

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_40756.1

Basepair signature

cWW-F-F-F

Number of instances in this motif group

14

Unit IDs

6IP8|1|1A|A|2420
6IP8|1|1A|G|2421
6IP8|1|1A|C|2422
6IP8|1|1A|A|2423
6IP8|1|1A|G|2424
6IP8|1|1A|U|2425
6IP8|1|1A|U|2426

Current chains

Chain 1A

28S ribosomal RNA

Nearby chains

Chain 2J

60S ribosomal protein L17

Chain 2L

60S ribosomal protein L19

Chain 2f

60S ribosomal protein L39