J4_9YDB_003

3D structure

PDB id

9YDB (explore in PDB, NAKB, or RNA 3D Hub)

Description

Eukaryotic pre-60S ribosomes from uL16 P-site loop mutants in bypass condition. Lsg1,Nmd3 and Tif6 present

Experimental method

ELECTRON MICROSCOPY

Resolution

2.83 Å

Loop

Sequence

CAAAUAU*AG*UGAU*AG

Length

15 nucleotides

Bulged bases

9YDB|1|A|A|1452, 9YDB|1|A|U|1455

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_9YDB_003 not in the Motif Atlas

Homologous match to J4_9PN5_003

Geometric discrepancy: 0.0816

The information below is about J4_9PN5_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_19484.2

Basepair signature

cWW-F-cWW-F-tSS-F-cWW-F-cWW

Number of instances in this motif group

9

Unit IDs

9YDB|1|A|C|1451
9YDB|1|A|A|1452
9YDB|1|A|A|1453
9YDB|1|A|A|1454
9YDB|1|A|U|1455
9YDB|1|A|A|1456
9YDB|1|A|U|1457
*
9YDB|1|A|A|1475
9YDB|1|A|G|1476
*
9YDB|1|A|U|1877
9YDB|1|A|G|1878
9YDB|1|A|A|1879
9YDB|1|A|U|1880
*
9YDB|1|A|A|2352
9YDB|1|A|G|2353

Current chains

Chain A

25S RNA

Nearby chains

Chain LR

60S ribosomal protein L17-A

Chain LT

60S ribosomal protein L19-A

Chain Lf

60S ribosomal protein L31-A