J3_4D5Y_044

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

AGAAG*CC*GAAAAU

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_4D5Y_044 not in the Motif Atlas

Homologous match to J3_8CRE_018

Geometric discrepancy: 0.2198

The information below is about J3_8CRE_018

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_12393.2

Basepair signature

cWW-tSH-tHH-F-F-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

4D5Y|1|2|A|2575
4D5Y|1|2|G|2576
4D5Y|1|2|A|2577
4D5Y|1|2|A|2578
4D5Y|1|2|G|2579
*
4D5Y|1|2|C|2714
4D5Y|1|2|C|2715
*
4D5Y|1|2|G|2719
4D5Y|1|2|A|2720
4D5Y|1|2|A|2721
4D5Y|1|2|A|2722
4D5Y|1|2|A|2723
4D5Y|1|2|U|2724

Current chains

Chain 2

28S Ribosomal RNA

Nearby chains

Chain A

60S RIBOSOMAL PROTEIN UL2

Chain g

60S RIBOSOMAL PROTEIN EL34

Chain p

60S RIBOSOMAL PROTEIN EL43