J3_5T6R_022

3D structure

PDB id

5T6R (explore in PDB, NAKB, or RNA 3D Hub)

Description

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex

Experimental method

ELECTRON MICROSCOPY

Resolution

4.2 Å

Loop

Sequence

AGAUGG*CGUUUCAAAGGC*GCCACCAU

Length

26 nucleotides

Bulged bases

5T6R|1|A|C|1556, 5T6R|1|A|A|1558, 5T6R|1|A|C|1581

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_5T6R_022 not in the Motif Atlas

Homologous match to J3_8P9A_056

Geometric discrepancy: 0.5933

The information below is about J3_8P9A_056

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_38098.1

Basepair signature

cWW-tSH-tWH-tWW-F-tHS-F-cWW-F-F-F-F-F-F-cWW-F-F-F

Number of instances in this motif group

1

Unit IDs

5T6R|1|A|A|1537
5T6R|1|A|G|1538
5T6R|1|A|A|1539
5T6R|1|A|U|1540
5T6R|1|A|G|1541
5T6R|1|A|G|1542
*
5T6R|1|A|C|1551
5T6R|1|A|G|1552
5T6R|1|A|U|1553
5T6R|1|A|U|1554
5T6R|1|A|U|1555
5T6R|1|A|C|1556
5T6R|1|A|A|1557
5T6R|1|A|A|1558
5T6R|1|A|A|1559
5T6R|1|A|G|1560
5T6R|1|A|G|1561
5T6R|1|A|C|1562
*
5T6R|1|A|G|1577
5T6R|1|A|C|1578
5T6R|1|A|C|1579
5T6R|1|A|A|1580
5T6R|1|A|C|1581
5T6R|1|A|C|1582
5T6R|1|A|A|1583
5T6R|1|A|U|1584

Current chains

Chain A

25S Ribosomal RNA

Nearby chains

Chain C

5.8S ribosomal RNA; 5.8S rRNA

Chain D

60S ribosomal protein L2-A

Chain J

60S ribosomal protein L8-A

Chain a

60S ribosomal protein L15-A

Chain k

60S ribosomal protein L25

Chain w

60S ribosomal protein L37-A