J5_5T62_006

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

UUGA*UUUG*CA*UG*CAGAAAA

Length

19 nucleotides

Bulged bases

5T62|1|A|G|2418, 5T62|1|A|A|2799, 5T62|1|A|G|2800, 5T62|1|A|A|2801, 5T62|1|A|A|2802

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_006 not in the Motif Atlas

Homologous match to J5_8P9A_015

Geometric discrepancy: 0.2035

The information below is about J5_8P9A_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_96125.1

Basepair signature

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

Number of instances in this motif group

6

Unit IDs

5T62|1|A|U|2416
5T62|1|A|U|2417
5T62|1|A|G|2418
5T62|1|A|A|2419
*
5T62|1|A|U|2611
5T62|1|A|U|2612
5T62|1|A|U|2613
5T62|1|A|G|2614
*
5T62|1|A|C|2627
5T62|1|A|A|2628
*
5T62|1|A|U|2650
5T62|1|A|G|2651
*
5T62|1|A|C|2798
5T62|1|A|A|2799
5T62|1|A|G|2800
5T62|1|A|A|2801
5T62|1|A|A|2802
5T62|1|A|A|2803
5T62|1|A|A|2804

Current chains

Chain A

25S Ribosomal RNA

Nearby chains

Chain D

60S ribosomal protein L2-A

Chain Q

60S ribosomal protein L42-A

Chain V

60S ribosomal export protein NMD3

Chain a

60S ribosomal protein L15-A

Chain d

60S ribosomal protein L18-A

Chain g

60S ribosomal protein L21-A

Chain n

60S ribosomal protein L28

Chain o

60S ribosomal protein L29