IL_8RJD_116

3D structure

PDB id

8RJD (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2

Experimental method

ELECTRON MICROSCOPY

Resolution

2.78574 Å

Loop

Sequence

GC*GCAU

Length

6 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

IL_8RJD_116 not in the Motif Atlas

Geometric match to IL_5TBW_089

Geometric discrepancy: 0.0841

The information below is about IL_5TBW_089

Detailed Annotation

Bulged stacked bases

Broad Annotation

Bulged stacked bases

Motif group

IL_22551.1

Basepair signature

cWW-L-cWW-L

Number of instances in this motif group

9

Unit IDs

8RJD|1|K|G|3780
8RJD|1|K|C|3781
*
8RJD|1|K|G|3811
8RJD|1|K|C|3812
8RJD|1|K|A|3813
8RJD|1|K|U|3814

Current chains

Chain K

28S rRNA

Nearby chains

Chain n

60S ribosomal protein L41

Chain q

Transfer RNA; tRNA