J4_8JDM_002

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

AUA(2MG)*C(M2G)(M2G)*UAG(G7M)(H2U)(5MC)G*CU

Length

16 nucleotides

Bulged bases

8JDM|1|C|U|8, 8JDM|1|C|H2U|47, 8JDM|1|C|5MC|48

QA status

Modified nucleotides: 2MG, M2G, G7M, H2U, 5MC

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

J4_8JDM_002 not in the Motif Atlas

Homologous match to J4_5AXM_001

Geometric discrepancy: 0.3327

The information below is about J4_5AXM_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.1

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

48

Unit IDs

8JDM|1|C|A|7
8JDM|1|C|U|8
8JDM|1|C|A|9
8JDM|1|C|2MG|10
*
8JDM|1|C|C|25
8JDM|1|C|M2G|26
8JDM|1|C|M2G|27
*
8JDM|1|C|U|43
8JDM|1|C|A|44
8JDM|1|C|G|45
8JDM|1|C|G7M|46
8JDM|1|C|H2U|47
8JDM|1|C|5MC|48
8JDM|1|C|G|49
*
8JDM|1|C|C|65
8JDM|1|C|U|66

Current chains

Chain C

tRNA (Tyr)

Nearby chains

Chain D

Large subunit ribosomal RNA; LSU rRNA

Chain O

60S ribosomal protein L10-like