J4_8RJD_011

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

GUAG*CGU*AAGGUCC*GC

Length

16 nucleotides

Bulged bases

8RJD|1|q|U|47, 8RJD|1|q|C|48

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

J4_8RJD_011 not in the Motif Atlas

Homologous match to J4_4WJ4_001

Geometric discrepancy: 0.2064

The information below is about J4_4WJ4_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_70449.29

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

54

Unit IDs

8RJD|1|q|G|7
8RJD|1|q|U|8
8RJD|1|q|A|9
8RJD|1|q|G|10
*
8RJD|1|q|C|25
8RJD|1|q|G|26
8RJD|1|q|U|27
*
8RJD|1|q|A|43
8RJD|1|q|A|44
8RJD|1|q|G|45
8RJD|1|q|G|46
8RJD|1|q|U|47
8RJD|1|q|C|48
8RJD|1|q|C|49
*
8RJD|1|q|G|65
8RJD|1|q|C|66

Current chains

Chain q

P-site tRNA

Nearby chains

Chain I

60S ribosomal protein L10

Chain K

Large subunit ribosomal RNA; LSU rRNA