HL_4D5Y_007

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

GUGUGAGGC

Length

9 nucleotides

Bulged bases

4D5Y|1|2|G|229, 4D5Y|1|2|U|230, 4D5Y|1|2|G|231

QA status

Unknown status

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_4D5Y_007 not in the Motif Atlas

Homologous match to HL_8C3A_007

Geometric discrepancy: 0.1838

The information below is about HL_8C3A_007

Detailed Annotation

T-loop with unstacked turn

Broad Annotation

T-loop

Motif group

HL_08002.12

Basepair signature

cWW-cWW-F-tWH

Number of instances in this motif group

16

Unit IDs

4D5Y|1|2|G|227
4D5Y|1|2|U|228
4D5Y|1|2|G|229
4D5Y|1|2|U|230
4D5Y|1|2|G|231
4D5Y|1|2|A|232
4D5Y|1|2|G|233
4D5Y|1|2|G|234
4D5Y|1|2|C|235

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 Y

60S RIBOSOMAL PROTEIN UL24