J5_5T62_003

3D structure

PDB id

5T62 (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-Tif6-Lsg1 Complex

Experimental method

ELECTRON MICROSCOPY

Resolution

3.1 Å

Loop

Sequence

CGAG*CGUAA*UGAACGUAG*CGA*UAAGAG

Length

27 nucleotides

Bulged bases

5T62|1|A|U|719, 5T62|1|A|A|784, 5T62|1|A|G|785

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_5T62_003 not in the Motif Atlas

Homologous match to J5_8P9A_012

Geometric discrepancy: 0.1057

The information below is about J5_8P9A_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_56629.1

Basepair signature

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

Number of instances in this motif group

3

Unit IDs

5T62|1|A|C|675
5T62|1|A|G|676
5T62|1|A|A|677
5T62|1|A|G|678
*
5T62|1|A|C|702
5T62|1|A|G|703
5T62|1|A|U|704
5T62|1|A|A|705
5T62|1|A|A|706
*
5T62|1|A|U|713
5T62|1|A|G|714
5T62|1|A|A|715
5T62|1|A|A|716
5T62|1|A|C|717
5T62|1|A|G|718
5T62|1|A|U|719
5T62|1|A|A|720
5T62|1|A|G|721
*
5T62|1|A|C|749
5T62|1|A|G|750
5T62|1|A|A|751
*
5T62|1|A|U|782
5T62|1|A|A|783
5T62|1|A|A|784
5T62|1|A|G|785
5T62|1|A|A|786
5T62|1|A|G|787

Current chains

Chain A

25S Ribosomal RNA

Nearby chains

Chain F

60S ribosomal protein L4-A

Chain N

60S ribosomal protein L13-A

Chain d

60S ribosomal protein L18-A

Chain n

60S ribosomal protein L28

Chain o

60S ribosomal protein L29

Chain v

60S ribosomal protein L36-A