J3_6IP8_025

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

CUUAAUUU*GGGAAACCUCAC*GGCUG

Length

25 nucleotides

Bulged bases

6IP8|1|2m|A|1240, 6IP8|1|2m|G|1256, 6IP8|1|2m|A|1258, 6IP8|1|2m|A|1260

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_025 not in the Motif Atlas

Homologous match to J3_8C3A_040

Geometric discrepancy: 0.1617

The information below is about J3_8C3A_040

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_83516.3

Basepair signature

cWW-F-F-F-tWW-F-tSH-tSS-cSS-F-F-F-F-F-cWW-cWW-F-F-F

Number of instances in this motif group

4

Unit IDs

6IP8|1|2m|C|1237
6IP8|1|2m|U|1238
6IP8|1|2m|U|1239
6IP8|1|2m|A|1240
6IP8|1|2m|A|1241
6IP8|1|2m|U|1242
6IP8|1|2m|U|1243
6IP8|1|2m|U|1244
*
6IP8|1|2m|G|1255
6IP8|1|2m|G|1256
6IP8|1|2m|G|1257
6IP8|1|2m|A|1258
6IP8|1|2m|A|1259
6IP8|1|2m|A|1260
6IP8|1|2m|C|1261
6IP8|1|2m|C|1262
6IP8|1|2m|U|1263
6IP8|1|2m|C|1264
6IP8|1|2m|A|1265
6IP8|1|2m|C|1266
*
6IP8|1|2m|G|1516
6IP8|1|2m|G|1517
6IP8|1|2m|C|1518
6IP8|1|2m|U|1519
6IP8|1|2m|G|1520

Current chains

Chain 2m

18S ribosomal RNA

Nearby chains

Chain 21

40S ribosomal protein S20

Chain 2w

40S ribosomal protein S15

Chain 2z

40S ribosomal protein S18

Chain 3E

40S ribosomal protein S29

Chain zw

Eukaryotic peptide chain release factor subunit 1