J5_4D5Y_002

3D structure

PDB id

4D5Y (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

Experimental method

ELECTRON MICROSCOPY

Resolution

9 Å

Loop

Sequence

GGAGUC*GGAC*GUUC*GCC*GCAGAUC

Length

24 nucleotides

Bulged bases

4D5Y|1|2|C|2265, 4D5Y|1|2|U|2327

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

J5_4D5Y_002 not in the Motif Atlas

Homologous match to J5_8C3A_002

Geometric discrepancy: 0.2011

The information below is about J5_8C3A_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

4D5Y|1|2|G|1315
4D5Y|1|2|G|1316
4D5Y|1|2|A|1317
4D5Y|1|2|G|1318
4D5Y|1|2|U|1319
4D5Y|1|2|C|1320
*
4D5Y|1|2|G|1495
4D5Y|1|2|G|1496
4D5Y|1|2|A|1497
4D5Y|1|2|C|1498
*
4D5Y|1|2|G|1637
4D5Y|1|2|U|1638
4D5Y|1|2|U|1639
4D5Y|1|2|C|1640
*
4D5Y|1|2|G|2264
4D5Y|1|2|C|2265
4D5Y|1|2|C|2266
*
4D5Y|1|2|G|2322
4D5Y|1|2|C|2323
4D5Y|1|2|A|2324
4D5Y|1|2|G|2325
4D5Y|1|2|A|2326
4D5Y|1|2|U|2327
4D5Y|1|2|C|2328

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain 3

5.8S ribosomal RNA; 5.8S rRNA

Chain C

60S RIBOSOMAL PROTEIN UL4

Chain L

60S RIBOSOMAL PROTEIN EL13

Chain N

60S RIBOSOMAL PROTEIN EL15

Chain a

60S RIBOSOMAL PROTEIN UL15

Chain e

60S RIBOSOMAL PROTEIN EL32

Chain t

60S RIBOSOMAL PROTEIN EL28