J5_8RJD_002

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

GGAGUC*GGAC*GUUC*GCC*GCAGAUC

Length

24 nucleotides

Bulged bases

8RJD|1|K|C|2289, 8RJD|1|K|U|2350

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

J5_8RJD_002 not in the Motif Atlas

Homologous match to J5_8P9A_011

Geometric discrepancy: 0.0573

The information below is about J5_8P9A_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_08384.1

Basepair signature

cWW-tSH-tSS-tHW-F-cWS-F-tWS-cWW-cWW-F-cWW-cWW-F

Number of instances in this motif group

4

Unit IDs

8RJD|1|K|G|1335
8RJD|1|K|G|1336
8RJD|1|K|A|1337
8RJD|1|K|G|1338
8RJD|1|K|U|1339
8RJD|1|K|C|1340
*
8RJD|1|K|G|1516
8RJD|1|K|G|1517
8RJD|1|K|A|1518
8RJD|1|K|C|1519
*
8RJD|1|K|G|1658
8RJD|1|K|U|1659
8RJD|1|K|U|1660
8RJD|1|K|C|1661
*
8RJD|1|K|G|2288
8RJD|1|K|C|2289
8RJD|1|K|C|2290
*
8RJD|1|K|G|2345
8RJD|1|K|C|2346
8RJD|1|K|A|2347
8RJD|1|K|G|2348
8RJD|1|K|A|2349
8RJD|1|K|U|2350
8RJD|1|K|C|2351

Current chains

Chain K

28S rRNA

Nearby chains

Chain C

Large ribosomal subunit protein uL4

Chain L

60S ribosomal protein L13

Chain N

Ribosomal protein L15

Chain a

60S ribosomal protein L27a

Chain e

Ribosomal protein L32

Chain r

60S ribosomal protein L28

Chain v

5.8S ribosomal RNA; 5.8S rRNA