J3_8RJD_017

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

UUGAAAAGAAC*GAGUUCAAGAGGGCG*CA

Length

28 nucleotides

Bulged bases

8RJD|1|K|G|409, 8RJD|1|K|G|413

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_8RJD_017 not in the Motif Atlas

Homologous match to J3_8C3A_049

Geometric discrepancy: 0.308

The information below is about J3_8C3A_049

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_91149.1

Basepair signature

cWW-cWS-tSH-F-tWH-cSS-cWW-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-F-cWW-cWW

Number of instances in this motif group

6

Unit IDs

8RJD|1|K|U|380
8RJD|1|K|U|381
8RJD|1|K|G|382
8RJD|1|K|A|383
8RJD|1|K|A|384
8RJD|1|K|A|385
8RJD|1|K|A|386
8RJD|1|K|G|387
8RJD|1|K|A|388
8RJD|1|K|A|389
8RJD|1|K|C|390
*
8RJD|1|K|G|401
8RJD|1|K|A|402
8RJD|1|K|G|403
8RJD|1|K|U|404
8RJD|1|K|U|405
8RJD|1|K|C|406
8RJD|1|K|A|407
8RJD|1|K|A|408
8RJD|1|K|G|409
8RJD|1|K|A|410
8RJD|1|K|G|411
8RJD|1|K|G|412
8RJD|1|K|G|413
8RJD|1|K|C|414
8RJD|1|K|G|415
*
8RJD|1|v|C|19
8RJD|1|v|A|20

Current chains

Chain K

28S rRNA

Chain v

5.8S rRNA

Nearby chains

Chain 1

Protein transport protein Sec61 subunit alpha isoform 1

Chain B

Nascent chain

Chain C

Large ribosomal subunit protein uL4

Chain P

uL22

Chain Y

Ribosomal protein L26

Chain l

60S ribosomal protein L39-like