J3_5GAK_027

3D structure

PDB id

5GAK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A

Experimental method

ELECTRON MICROSCOPY

Resolution

3.88 Å

Loop

Sequence

AGCU*ACGUUCUAGCAUUCAAG*UGAU

Length

25 nucleotides

Bulged bases

5GAK|1|1|G|2549, 5GAK|1|1|U|2550, 5GAK|1|1|U|2551, 5GAK|1|1|A|2554, 5GAK|1|1|U|2558, 5GAK|1|1|U|2559, 5GAK|1|1|C|2560

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_5GAK_027 not in the Motif Atlas

Homologous match to J3_8CRE_020

Geometric discrepancy: 0.2132

The information below is about J3_8CRE_020

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_28639.1

Basepair signature

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

Number of instances in this motif group

2

Unit IDs

5GAK|1|1|A|2529
5GAK|1|1|G|2530
5GAK|1|1|C|2531
5GAK|1|1|U|2532
*
5GAK|1|1|A|2547
5GAK|1|1|C|2548
5GAK|1|1|G|2549
5GAK|1|1|U|2550
5GAK|1|1|U|2551
5GAK|1|1|C|2552
5GAK|1|1|U|2553
5GAK|1|1|A|2554
5GAK|1|1|G|2555
5GAK|1|1|C|2556
5GAK|1|1|A|2557
5GAK|1|1|U|2558
5GAK|1|1|U|2559
5GAK|1|1|C|2560
5GAK|1|1|A|2561
5GAK|1|1|A|2562
5GAK|1|1|G|2563
*
5GAK|1|1|U|2578
5GAK|1|1|G|2579
5GAK|1|1|A|2580
5GAK|1|1|U|2581

Current chains

Chain 1

25S rRNA

Nearby chains

Chain D

60S ribosomal protein L43-A

Chain E

60S ribosomal protein L2-A

Chain K

60S ribosomal protein L8-A

Chain Z

60S ribosomal protein L25

Chain b

60S ribosomal protein L27-A

Chain e

60S ribosomal protein L30

Chain i

60S ribosomal protein L34-A