IL_8JDM_124

3D structure

PDB id

8JDM (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (rotated state)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.67 Å

Loop

Sequence

C(5MC)AA(A2M)UGCCUC(OMG)U*A(OMC)GCG

Length

18 nucleotides

Bulged bases

8JDM|1|D|C|3791, 8JDM|1|D|C|3810

QA status

Modified nucleotides: 5MC, A2M, OMG, OMC

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

IL_8JDM_124 not in the Motif Atlas

Homologous match to IL_5TBW_090

Geometric discrepancy: 0.5034

The information below is about IL_5TBW_090

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_66080.1

Basepair signature

cWW-cWW-tSH-L-cWW-L

Number of instances in this motif group

5

Unit IDs

8JDM|1|D|C|3781
8JDM|1|D|5MC|3782
8JDM|1|D|A|3783
8JDM|1|D|A|3784
8JDM|1|D|A2M|3785
8JDM|1|D|U|3786
8JDM|1|D|G|3787
8JDM|1|D|C|3788
8JDM|1|D|C|3789
8JDM|1|D|U|3790
8JDM|1|D|C|3791
8JDM|1|D|OMG|3792
8JDM|1|D|U|3793
*
8JDM|1|D|A|3807
8JDM|1|D|OMC|3808
8JDM|1|D|G|3809
8JDM|1|D|C|3810
8JDM|1|D|G|3811

Current chains

Chain D

28S ribosomal RNA

Nearby chains

Chain C

Transfer RNA; tRNA

Chain s

60S ribosomal protein L41

Chain w

Small subunit ribosomal RNA; SSU rRNA